Modules: Difference between revisions

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This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the ''module avail'' command for the official list of software modules installed on Cheaha.
This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the ''module avail'' command for the official list of software modules installed on Cheaha.


Last Update: 2019-04-09
Last Update: 2019-06-13
__NOTOC__
__NOTOC__
<p class="toc">'''Contents:'''  | [[#A|A]] | [[#B|B]] | [[#C|C]] | [[#D|D]] | [[#E|E]] | [[#F|F]] | [[#G|G]] | [[#H|H]] | [[#I|I]] | [[#J|J]] | [[#K|K]] | [[#L|L]] | [[#M|M]] | [[#N|N]] | [[#O|O]] | [[#P|P]] | [[#Q|Q]] | [[#R|R]] | [[#S|S]] | [[#T|T]] | [[#U|U]] | [[#V|V]] | [[#W|W]] | [[#X|X]] | [[#Y|Y]] | [[#Z|Z]]</p>
<p class="toc">'''Contents:'''  | [[#A|A]] | [[#B|B]] | [[#C|C]] | [[#D|D]] | [[#E|E]] | [[#F|F]] | [[#G|G]] | [[#H|H]] | [[#I|I]] | [[#J|J]] | [[#K|K]] | [[#L|L]] | [[#M|M]] | [[#N|N]] | [[#O|O]] | [[#P|P]] | [[#Q|Q]] | [[#R|R]] | [[#S|S]] | [[#T|T]] | [[#U|U]] | [[#V|V]] | [[#W|W]] | [[#X|X]] | [[#Y|Y]] | [[#Z|Z]]</p>
Line 131: Line 131:
|[[#Bismark|'''Bismark''']]
|[[#Bismark|'''Bismark''']]
|0.19.0-foss-2016a
|0.19.0-foss-2016a
|- style="vertical-align:top;"
|[[#Bison|'''Bison''']]
|3.0.4-GCCcore-7.3.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 344: Line 340:


|[[#dvctools|'''dvctools''']]
|[[#dvctools|'''dvctools''']]
|1.0
|recommended
|}
|}
==E==
==E==
Line 471: Line 467:
|[[#flex|'''flex''']]
|[[#flex|'''flex''']]
|2.6.3-GCCcore-7.3.0
|2.6.3-GCCcore-7.3.0
|- style="vertical-align:top;"
|[[#fontconfig|'''fontconfig''']]
|2.12.1-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 483: Line 475:
|[[#freeglut|'''freeglut''']]
|[[#freeglut|'''freeglut''']]
|3.0.0-intel-2017a
|3.0.0-intel-2017a
|- style="vertical-align:top;"
|[[#freetype|'''freetype''']]
|2.6.5-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 566: Line 554:
|[[#GDAL|'''GDAL''']]
|[[#GDAL|'''GDAL''']]
|2.2.3-foss-2018a-Python-3.6.4
|2.2.3-foss-2018a-Python-3.6.4
|- style="vertical-align:top;"
|[[#GMP|'''GMP''']]
|6.1.2-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 578: Line 562:
|[[#GObject-Introspection|'''GObject-Introspection''']]
|[[#GObject-Introspection|'''GObject-Introspection''']]
|1.48.0-foss-2016a
|1.48.0-foss-2016a
|- style="vertical-align:top;"
|[[#GSL|'''GSL''']]
|1.16-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 590: Line 570:
|[[#Gdk-Pixbuf|'''Gdk-Pixbuf''']]
|[[#Gdk-Pixbuf|'''Gdk-Pixbuf''']]
|2.36.10-intel-2017a
|2.36.10-intel-2017a
|- style="vertical-align:top;"
|[[#Ghostscript|'''Ghostscript''']]
|9.19-intel-2016a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 602: Line 578:
|[[#gcccuda|'''gcccuda''']]
|[[#gcccuda|'''gcccuda''']]
|2018b
|2018b
|- style="vertical-align:top;"
|[[#gettext|'''gettext''']]
|0.19.8-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 622: Line 594:
|[[#goolf|'''goolf''']]
|[[#goolf|'''goolf''']]
|1.7.20
|1.7.20
|- style="vertical-align:top;"
|[[#gperf|'''gperf''']]
|3.0.4-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 768: Line 736:
|[[#IPython|'''IPython''']]
|[[#IPython|'''IPython''']]
|5.0.0-foss-2016a-Python-3.5.1
|5.0.0-foss-2016a-Python-3.5.1
|- style="vertical-align:top;"
|[[#ImageMagick|'''ImageMagick''']]
|7.0.2-5-intel-2016a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 804: Line 768:
|[[#intel|'''intel''']]
|[[#intel|'''intel''']]
|mic/sdk/3.8.4
|mic/sdk/3.8.4
|- style="vertical-align:top;"
|[[#intltool|'''intltool''']]
|0.51.0-GCCcore-5.4.0-Perl-5.24.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 847: Line 807:
|[[#JUnit|'''JUnit''']]
|[[#JUnit|'''JUnit''']]
|4.12-Java-1.8.0_92
|4.12-Java-1.8.0_92
|- style="vertical-align:top;"
|[[#JasPer|'''JasPer''']]
|2.0.14-GCCcore-6.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 921: Line 877:
|[[#LAPACK|'''LAPACK''']]
|[[#LAPACK|'''LAPACK''']]
|3.4.2-gompi-1.5.12
|3.4.2-gompi-1.5.12
|- style="vertical-align:top;"
|[[#LLVM|'''LLVM''']]
|3.7.1-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 933: Line 885:
|[[#LibTIFF|'''LibTIFF''']]
|[[#LibTIFF|'''LibTIFF''']]
|4.0.9-GCCcore-5.4.0
|4.0.9-GCCcore-5.4.0
|- style="vertical-align:top;"
|[[#LittleCMS|'''LittleCMS''']]
|2.7-intel-2016a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,041: Line 989:
|[[#libdrm|'''libdrm''']]
|[[#libdrm|'''libdrm''']]
|2.4.91-GCCcore-5.4.0
|2.4.91-GCCcore-5.4.0
|- style="vertical-align:top;"
|[[#libffi|'''libffi''']]
|3.2.1-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,081: Line 1,025:
|[[#libpciaccess|'''libpciaccess''']]
|[[#libpciaccess|'''libpciaccess''']]
|0.13.4-intel-2016a
|0.13.4-intel-2016a
|- style="vertical-align:top;"
|[[#libpng|'''libpng''']]
|1.6.24-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


|[[#libpthread-stubs|'''libpthread-stubs''']]
|[[#libpthread-stubs|'''libpthread-stubs''']]
|0.3-intel-2016a
|0.3-intel-2016a
|- style="vertical-align:top;"
|[[#libreadline|'''libreadline''']]
|7.0-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,191: Line 1,127:


|[[#matlab|'''matlab''']]
|[[#matlab|'''matlab''']]
|R2017b
|R2019a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


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|[[#MVAPICH2|'''MVAPICH2''']]
|[[#MVAPICH2|'''MVAPICH2''']]
|2.2b-GCC-4.9.3-2.25
|2.2b-GCC-4.9.3-2.25
|- style="vertical-align:top;"
|[[#Mako|'''Mako''']]
|1.0.7-foss-2016b-Python-2.7.14
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,347: Line 1,279:
|[[#ncdu|'''ncdu''']]
|[[#ncdu|'''ncdu''']]
|1.13-20.1
|1.13-20.1
|- style="vertical-align:top;"
|[[#nighres|'''nighres''']]
|1.1.0b1
|- style="vertical-align:top;"
|- style="vertical-align:top;"


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|[[#ncbi-vdb|'''ncbi-vdb''']]
|[[#ncbi-vdb|'''ncbi-vdb''']]
|2.7.0-foss-2016b
|2.7.0-foss-2016b
|- style="vertical-align:top;"
|[[#netCDF-Fortran|'''netCDF-Fortran''']]
|4.4.4-intel-2016a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


|[[#netCDF|'''netCDF''']]
|[[#netCDF|'''netCDF''']]
|4.6.0-foss-2018a
|4.6.0-foss-2018a
|- style="vertical-align:top;"
|[[#nettle|'''nettle''']]
|3.4-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


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|[[#perl-app-cpanminus|'''perl-app-cpanminus''']]
|[[#perl-app-cpanminus|'''perl-app-cpanminus''']]
|1.7039
|1.7039
|- style="vertical-align:top;"
|[[#picard|'''picard''']]
|2.10.0-Java-1.8.0_74
|- style="vertical-align:top;"
|- style="vertical-align:top;"


|[[#pixman|'''pixman''']]
|[[#pixman|'''pixman''']]
|0.34.0-GCCcore-5.4.0
|0.34.0-GCCcore-5.4.0
|- style="vertical-align:top;"
|[[#pkg-config|'''pkg-config''']]
|0.29.2-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,702: Line 1,622:
!Latest version
!Latest version


|- style="vertical-align:top;"
|[[#snakemakeslurm_local|'''snakemakeslurm_local''']]
|4.8.0-1
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,726: Line 1,650:
|[[#S.A.G.E.|'''S.A.G.E.''']]
|[[#S.A.G.E.|'''S.A.G.E.''']]
|6.3
|6.3
|- style="vertical-align:top;"
|[[#SAMtools|'''SAMtools''']]
|1.4.1-intel-2017a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,754: Line 1,674:
|[[#SPPARKS|'''SPPARKS''']]
|[[#SPPARKS|'''SPPARKS''']]
|07192016-intel-2016a
|07192016-intel-2016a
|- style="vertical-align:top;"
|[[#SQLite|'''SQLite''']]
|3.21.0-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,770: Line 1,686:
|[[#SWIG|'''SWIG''']]
|[[#SWIG|'''SWIG''']]
|3.0.12-foss-2018a-Python-2.7.14
|3.0.12-foss-2018a-Python-2.7.14
|- style="vertical-align:top;"
|[[#Salmon|'''Salmon''']]
|0.9.1-foss-2016b-Python-2.7.12
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,857: Line 1,769:
|[[#Tar|'''Tar''']]
|[[#Tar|'''Tar''']]
|1.29-goolf-1.4.10
|1.29-goolf-1.4.10
|- style="vertical-align:top;"
|[[#Tcl|'''Tcl''']]
|8.6.8-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,885: Line 1,793:
|[[#tabix|'''tabix''']]
|[[#tabix|'''tabix''']]
|0.2.6-intel-2015b
|0.2.6-intel-2015b
|- style="vertical-align:top;"
|[[#tbb|'''tbb''']]
|2017_U5-foss-2016b
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,924: Line 1,828:
!Latest version
!Latest version


|- style="vertical-align:top;"
|[[#util-linux|'''util-linux''']]
|2.31.1-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 1,997: Line 1,897:
|[[#xget|'''xget''']]
|[[#xget|'''xget''']]
|xget-public
|xget-public
|- style="vertical-align:top;"
|[[#X11|'''X11''']]
|20180131-GCCcore-5.4.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


|[[#XKeyboardConfig|'''XKeyboardConfig''']]
|[[#XKeyboardConfig|'''XKeyboardConfig''']]
|2.17-intel-2016a
|2.17-intel-2016a
|- style="vertical-align:top;"
|[[#XML-Parser|'''XML-Parser''']]
|2.44_01-GCCcore-5.4.0-Perl-5.24.0
|- style="vertical-align:top;"
|- style="vertical-align:top;"


Line 2,099: Line 1,991:
!Latest version
!Latest version


|- style="vertical-align:top;"
|[[#zlib|'''zlib''']]
|1.2.9-intel-2017a
|- style="vertical-align:top;"
|- style="vertical-align:top;"


|[[#ZeroMQ|'''ZeroMQ''']]
|[[#ZeroMQ|'''ZeroMQ''']]
|4.1.4-foss-2016a
|4.1.4-foss-2016a
|- style="vertical-align:top;"
|[[#zlib|'''zlib''']]
|1.2.9-intel-2017a
|}
|}
==Software Detail==
==Software Detail==
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Command: ''module load Bismark''
Command: ''module load Bismark''
===Bison===
Homepage: http://www.gnu.org/software/bison
Description: Bison is a general-purpose parser generator that converts an annotated context-free grammarinto a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
Available versions: 2.7-foss-2016a, 3.0.2-intel-2015b, 3.0.4, 3.0.4-GCC-4.9.3-2.25, 3.0.4-GCC-4.9.3-binutils-2.25, 3.0.4-GCCcore-4.9.3, 3.0.4-GCCcore-5.4.0, 3.0.4-GCCcore-6.3.0, 3.0.4-foss-2016a, 3.0.4-foss-2016b, 3.0.4-goolf-1.7.20, 3.0.4-intel-2015b, 3.0.4-intel-2016a, 3.0.4-GCCcore-6.1.0, 2.7-GCCcore-6.3.0, 2.7, 3.0.4-GCCcore-6.4.0, 3.0.4-intel-2017a, 3.0.4-GCCcore-7.3.0
Command: ''module load Bison''


===Bowtie===
===Bowtie===
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===dvctools===
===dvctools===


Available versions: 0.3, recommended, 0.4, 0.5, 0.6, 0.7, 0.8, latest, 0.9, 0.2, 1.0
Available versions: 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.2, 1.0, latest, recommended


Command: ''module load dvctools''
Command: ''module load dvctools''
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Command: ''module load flex''
Command: ''module load flex''
===fontconfig===
Homepage: http://www.freedesktop.org/software/fontconfig
Description: Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
Available versions: 2.11.1-intel-2015b, 2.11.1-intel-2016a, 2.11.94-foss-2016a, 2.11.94-foss-2016b, 2.11.95-intel-2016a, 2.12.1-foss-2016b, 2.12.1-intel-2015b, 2.12.1-intel-2016a, 2.12.1-GCCcore-6.3.0-libpng-1.6.29, 2.12.4-GCCcore-6.4.0, 2.12.1-intel-2017a, 2.11.94-intel-2016a, 2.11.95-foss-2016b, 2.11.95-foss-2016a, 2.12.6-GCCcore-6.4.0, 2.12.1-GCCcore-5.4.0-libpng-1.6.29, 2.12.6-GCCcore-5.4.0, 2.12.1-GCCcore-5.4.0
Command: ''module load fontconfig''


===fontsproto===
===fontsproto===
Line 2,913: Line 2,785:


Command: ''module load freeglut''
Command: ''module load freeglut''
===freetype===
Homepage: http://freetype.org
Description: FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, andportable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, displayservers, font conversion tools, text image generation tools, and many other products as well.
Available versions: 2.5.3-intel-2015b, 2.6-intel-2015b, 2.6.2-foss-2016a, 2.6.2-foss-2016b, 2.6.2-goolf-1.7.20, 2.6.2-intel-2016a, 2.6.3-foss-2016a, 2.6.3-intel-2016a, 2.6.5-foss-2016b, 2.6.5-intel-2015b, 2.6.5-intel-2016a, 2.7-foss-2016b, 2.7.1-GCCcore-6.3.0-libpng-1.6.29, 2.7.1-goolf-1.7.20-libpng-1.6.18, 2.8-GCCcore-6.4.0, 2.6.5-intel-2017a, 2.6.3-foss-2016b, 2.6.5-intel-2016b, 2.6-intel-2016a, 2.6-intel-2016b, 2.6.2-intel-2016b, 2.9-GCCcore-6.4.0, 2.7.1-GCCcore-5.4.0-libpng-1.6.29, 2.9-GCCcore-5.4.0, 2.6.5-GCCcore-5.4.0
Command: ''module load freetype''


===FastQ_Screen===
===FastQ_Screen===
Line 3,067: Line 2,929:


Command: ''module load GDAL''
Command: ''module load GDAL''
===GMP===
Homepage: http://gmplib.org/
Description: GMP is a free library for arbitrary precision arithmetic,operating on signed integers, rational numbers, and floating point numbers.
Available versions: 5.0.5-goolf-1.4.10, 5.0.5-goolf-1.7.20, 6.0.0a-GCC-4.8.4, 6.0.0a-GNU-4.9.3-2.25, 6.1.0-foss-2016a, 6.1.0-foss-2016b, 6.1.0-goolf-1.7.20, 6.1.0-intel-2015b, 6.1.0-intel-2016a, 6.1.1-foss-2016a, 6.1.1-foss-2016b, 6.1.1-intel-2015b, 6.1.1-intel-2016a, 6.1.2-GCCcore-6.3.0, 6.1.1-intel-2017a, 6.1.2-GCCcore-6.4.0, 4.3.2, 6.1.2-GCCcore-5.4.0
Command: ''module load GMP''


===GNU===
===GNU===
Line 3,094: Line 2,946:
Command: ''module load GObject-Introspection''
Command: ''module load GObject-Introspection''


===GSL===
===GTK+===


Homepage: http://www.gnu.org/software/gsl/
Homepage: https://developer.gnome.org/gtk+/stable/
 
Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.The library provides a wide range of mathematical routines such as random number generators, special functionsand least-squares fitting.
 
Available versions: 1.16-goolf-1.7.20, 1.16-intel-2015b, 2.1-foss-2015b, 2.1-foss-2016a, 2.1-intel-2016a, 2.3-foss-2016b, 1.16-foss-2016b
 
Command: ''module load GSL''
 
===GTK+===
 
Homepage: https://developer.gnome.org/gtk+/stable/


Description: The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
Description: The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
Line 3,123: Line 2,965:


Command: ''module load Gdk-Pixbuf''
Command: ''module load Gdk-Pixbuf''
===Ghostscript===
Available versions: 9.19-intel-2016a
Command: ''module load Ghostscript''


===gawk===
===gawk===
Line 3,145: Line 2,981:


Command: ''module load gcccuda''
Command: ''module load gcccuda''
===gettext===
Homepage: http://www.gnu.org/software/gettext/
Description: GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we maybuild many other steps. This package offers to programmers, translators, and even users, a well integrated set of toolsand documentation
Available versions: 0.19.2-goolf-1.7.20, 0.19.2-intel-2015b, 0.19.6-GNU-4.9.3-2.25, 0.19.6-foss-2016a, 0.19.6-foss-2016b, 0.19.6-intel-2015b, 0.19.6-intel-2016a, 0.19.7-intel-2016a, 0.19.8, 0.19.8-foss-2016a, 0.19.8-foss-2016b, 0.19.8-intel-2015b, 0.19.8-intel-2016a, 0.19.8.1, 0.19.8.1-GCCcore-6.3.0, 0.19.6, 0.19.8.1-GCCcore-6.4.0, 0.19.8-intel-2017a, 0.19.4-intel-2015b, 0.19.7-foss-2016b, 0.19.7-foss-2016a, 0.19.8.1-GCCcore-6.4.0-libxml2-2.9.7, 0.19.8.1-GCCcore-5.4.0, 0.19.8.1-GCCcore-5.4.0-libxml2-2.9.7, 0.19.8-GCCcore-5.4.0
Command: ''module load gettext''


===glproto===
===glproto===
Line 3,183: Line 3,009:


Command: ''module load goolf''
Command: ''module load goolf''
===gperf===
Homepage: http://www.gnu.org/software/gperf/
Description: GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hashfunction and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hashfunction is perfect, which means that the hash table has no collisions, and the hash table lookup needs a singlestring comparison only.
Available versions: 3.0.4-goolf-1.7.20, 3.0.4-intel-2016a, 3.1-GCCcore-6.4.0, 3.1-GCCcore-5.4.0, 3.0.4-foss-2016b
Command: ''module load gperf''


===grep===
===grep===
Line 3,425: Line 3,241:


Command: ''module load IPython''
Command: ''module load IPython''
===ImageMagick===
Available versions: 7.0.2-5-intel-2016a
Command: ''module load ImageMagick''


===icc===
===icc===
Line 3,503: Line 3,313:


Command: ''module load intel''
Command: ''module load intel''
===intltool===
Homepage: http://freedesktop.org/wiki/Software/intltool/
Description: intltool is a set of tools to centralize translation ofmany different file formats using GNU gettext-compatible PO files.
Available versions: 0.51.0-intel-2016a-Perl-5.22.1, 0.51.0-intel-2017a-Perl-5.24.1, 0.51.0-GCCcore-6.4.0-Perl-5.26.0, 0.51.0-GCCcore-6.4.0-Perl-5.26.1, 0.51.0-GCCcore-5.4.0-Perl-5.26.1, 0.51.0-GCCcore-5.4.0-Perl-5.24.0
Command: ''module load intltool''


===ITK===
===ITK===
Line 3,569: Line 3,369:


Command: ''module load JUnit''
Command: ''module load JUnit''
===JasPer===
Homepage: http://www.ece.uvic.ca/~frodo/jasper/
Description: The JasPer Project is an open-source initiative to provide a freesoftware-based reference implementation of the codec specified inthe JPEG-2000 Part-1 standard.
Available versions: 1.900.1-intel-2016a, 1.900.1-intel-2017a, 1.900.1-foss-2016b, 2.0.14-GCCcore-6.4.0
Command: ''module load JasPer''


===Java===
===Java===
Line 3,675: Line 3,465:


Command: ''module load LAPACK''
Command: ''module load LAPACK''
===LLVM===
Homepage: http://llvm.org/
Description: The LLVM Core libraries provide a modern source- and target-independentoptimizer, along with code generation support for many popular CPUs(as well as some less common ones!) These libraries are built around a wellspecified code representation known as the LLVM intermediate representation("LLVM IR"). The LLVM Core libraries are well documented, and it isparticularly easy to invent your own language (or port an existing compiler)to use LLVM as an optimizer and code generator.
Available versions: 3.7.1-intel-2016a, 3.8.0-intel-2016a, 3.8.1-foss-2016b, 4.0.0-intel-2017a, 5.0.1-GCCcore-6.4.0, 5.0.1-GCCcore-5.4.0, 3.7.1-foss-2016b
Command: ''module load LLVM''


===LeadIT===
===LeadIT===
Line 3,701: Line 3,481:


Command: ''module load LibTIFF''
Command: ''module load LibTIFF''
===LittleCMS===
Available versions: 2.7-intel-2016a
Command: ''module load LittleCMS''


===Lmod===
===Lmod===
Line 3,885: Line 3,659:


Command: ''module load libdrm''
Command: ''module load libdrm''
===libffi===
Homepage: http://sourceware.org/libffi/
Description: The libffi library provides a portable, high level programming interface to various callingconventions. This allows a programmer to call any function specified by a call interface description at run-time.
Available versions: 3.1-goolf-1.7.20, 3.1-intel-2015b, 3.2.1-GNU-4.9.3-2.25, 3.2.1-foss-2016a, 3.2.1-foss-2016b, 3.2.1-intel-2015b, 3.2.1-intel-2016a, 3.2.1-GCCcore-6.3.0, 3.2.1-intel-2017a, 3.2.1-GCCcore-6.4.0, 3.2.1-intel-2016b, 3.2.1-GCCcore-5.4.0
Command: ''module load libffi''


===libfontenc===
===libfontenc===
Line 3,966: Line 3,730:
Command: ''module load libpciaccess''
Command: ''module load libpciaccess''


===libpng===
===libpthread-stubs===
 
Homepage: http://www.libpng.org/pub/png/libpng.html
 
Description: libpng is the official PNG reference library
 
Available versions: 1.5.13-goolf-1.7.20, 1.6.10-intel-2015b, 1.6.10-intel-2016a, 1.6.12-intel-2015b, 1.6.12-intel-2016a, 1.6.16-goolf-1.7.20, 1.6.16-intel-2015b, 1.6.17-foss-2015b, 1.6.17-goolf-1.7.20, 1.6.17-intel-2015b, 1.6.2-goolf-1.4.10, 1.6.2-goolf-1.7.20, 1.6.21-foss-2016a, 1.6.21-foss-2016b, 1.6.21-goolf-1.7.20, 1.6.21-intel-2015b, 1.6.21-intel-2016a, 1.6.23-foss-2016a, 1.6.23-foss-2016b, 1.6.23-intel-2015b, 1.6.23-intel-2016a, 1.6.24-foss-2016b, 1.6.24-intel-2015b, 1.6.24-intel-2016a, 1.6.26-foss-2016b, 1.6.29-intel-2016a, 1.6.29-GCCcore-6.3.0, 1.6.18-goolf-1.7.20, 1.6.32-GCCcore-6.4.0, 1.6.24-intel-2017a, 1.6.24-intel-2016b, 1.6.17-intel-2016a, 1.6.17-intel-2016b, 1.6.21-intel-2016b, 1.6.34-GCCcore-6.4.0, 1.6.29-GCCcore-5.4.0, 1.6.34-GCCcore-5.4.0, 1.6.24-GCCcore-5.4.0
 
Command: ''module load libpng''
 
===libpthread-stubs===


Available versions: 0.3-foss-2015b, 0.3-foss-2016a, 0.3-foss-2016b, 0.3-goolf-1.7.20, 0.3-intel-2015b, 0.3-intel-2016a
Available versions: 0.3-foss-2015b, 0.3-foss-2016a, 0.3-foss-2016b, 0.3-goolf-1.7.20, 0.3-intel-2015b, 0.3-intel-2016a


Command: ''module load libpthread-stubs''
Command: ''module load libpthread-stubs''
===libreadline===
Homepage: http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html
Description: The GNU Readline library provides a set of functions for use by applications thatallow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available.The Readline library includes additional functions to maintain a list of previously-entered command lines,to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Available versions: 6.2-foss-2016a, 6.2-goolf-1.4.10, 6.2-goolf-1.7.20, 6.3-GNU-4.9.3-2.25, 6.3-foss-2015b, 6.3-foss-2016a, 6.3-foss-2016b, 6.3-goolf-1.7.20, 6.3-intel-2015b, 6.3-intel-2016a, 7.0-GCCcore-6.3.0, 6.2-intel-2016a, 6.3-intel-2017a, 7.0-GCCcore-6.4.0, 7.0-GCCcore-5.4.0
Command: ''module load libreadline''


===libsodium===
===libsodium===
Line 4,170: Line 3,914:
===matlab===
===matlab===


Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b
Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b, R2019a


Command: ''module load rc/matlab''
Command: ''module load rc/matlab''
Line 4,263: Line 4,007:


Command: ''module load MVAPICH2''
Command: ''module load MVAPICH2''
===Mako===
Homepage: http://www.makotemplates.org
Description: A super-fast templating language that borrows the best ideas from the existing templating languages
Available versions: 1.0.4-foss-2016b-Python-2.7.12, 1.0.6-intel-2017a-Python-2.7.13, 1.0.7-foss-2018a-Python-2.7.14, 1.0.7-foss-2016b-Python-2.7.14
Command: ''module load Mako''


===Maq===
===Maq===
Line 4,457: Line 4,191:


Command: ''module load rc/ncdu''
Command: ''module load rc/ncdu''
===nighres===
Available versions: 1.1.0b1
Command: ''module load rc/nighres''


===NASM===
===NASM===
Line 4,479: Line 4,219:


Command: ''module load ncbi-vdb''
Command: ''module load ncbi-vdb''
===netCDF-Fortran===
Available versions: 4.4.4-intel-2016a
Command: ''module load netCDF-Fortran''


===netCDF===
===netCDF===
Line 4,495: Line 4,229:


Command: ''module load netCDF''
Command: ''module load netCDF''
===nettle===
Homepage: http://www.lysator.liu.se/~nisse/nettle/
Description: Nettle is a cryptographic library that is designed to fit easilyin more or less any context: In crypto toolkits for object-orientedlanguages (C++, Python, Pike, ...), in applications like LSH or GNUPG,or even in kernel space.
Available versions: 3.1.1-GNU-4.9.3-2.25, 3.2-foss-2016b, 3.2-intel-2016a, 3.3-intel-2017a, 3.3-GCCcore-6.4.0, 3.2-intel-2017a, 3.4-foss-2018a, 3.3-foss-2016b, 3.4-foss-2016b
Command: ''module load nettle''


===nodejs===
===nodejs===
Line 4,795: Line 4,519:


Command: ''module load perl-app-cpanminus''
Command: ''module load perl-app-cpanminus''
===picard===
Available versions: 2.1.1-Java-1.8.0_74, 2.10.0-Java-1.8.0_74
Command: ''module load picard''


===pixman===
===pixman===
Line 4,811: Line 4,529:


Command: ''module load pixman''
Command: ''module load pixman''
===pkg-config===
Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
Description: pkg-config is a helper tool used when compiling applications and libraries. It helps you insert thecorrect compiler options on the command line so an application can usegcc -o test test.c `pkg-config --libs --cflags glib-2.0`for instance, rather than hard-coding values on where to find glib (or other libraries).
Available versions: 0.28-GNU-4.9.3-2.25, 0.29-foss-2016a, 0.29-foss-2016b, 0.29-goolf-1.7.20, 0.29-intel-2016a, 0.29.1-foss-2016b, 0.29.1-intel-2015b, 0.29.1-intel-2016a, 0.29.1-GCCcore-6.3.0, 0.29.1-intel-2017a, 0.29.2-GCCcore-6.4.0, 0.29.2-GCCcore-5.4.0, 0.29.1-GCCcore-5.4.0, 0.29.2-foss-2016b
Command: ''module load pkg-config''


===pkgconfig===
===pkgconfig===
Line 5,073: Line 4,781:


Command: ''module load Rust''
Command: ''module load Rust''
===snakemakeslurm_local===
Available versions: 4.8.0-1
Command: ''module load snakemakeslurm_local''


===SAS===
===SAS===
Line 5,109: Line 4,823:


Command: ''module load S.A.G.E.''
Command: ''module load S.A.G.E.''
===SAMtools===
Homepage: http://www.htslib.org/
Description: SAM Tools provide various utilities for manipulating alignments in the SAM format,including sorting, merging, indexing and generating alignments in a per-position format.
Available versions: 0.1.19-foss-2016a, 0.1.19-goolf-1.7.20, 1.3.1-foss-2016a, 1.3.1-intel-2015b, 1.5-intel-2017a, 1.6-intel-2017a, 1.6-intel-2016a, 1.3.1-intel-2017a-HTSlib-1.3.2, 1.4.1-intel-2017a
Command: ''module load SAMtools''


===SCOTCH===
===SCOTCH===
Line 5,159: Line 4,863:


Command: ''module load SPPARKS''
Command: ''module load SPPARKS''
===SQLite===
Homepage: http://www.sqlite.org/
Description: SQLite: SQL Database Engine in a C Library
Available versions: 3.13.0-foss-2016a, 3.13.0-foss-2016b, 3.13.0-intel-2015b, 3.13.0-intel-2016a, 3.8.10.2-goolf-1.7.20, 3.8.10.2-intel-2015b, 3.8.8.1-foss-2015b, 3.8.8.1-goolf-1.7.20, 3.8.8.1-intel-2015b, 3.9.2-foss-2016a, 3.9.2-foss-2016b, 3.9.2-goolf-1.7.20, 3.9.2-intel-2015b, 3.9.2-intel-2016a, 3.17.0-GCCcore-6.3.0, 3.8.9-foss-2016a, 3.8.5-goolf-1.4.10, 3.8.5-intel-2016a, 3.13.0-intel-2017a, 3.20.1-GCCcore-6.4.0, 3.21.0-GCCcore-6.4.0, 3.17.0-GCCcore-5.4.0, 3.20.1-GCCcore-5.4.0, 3.21.0-GCCcore-5.4.0
Command: ''module load SQLite''


===STAR-Fusion===
===STAR-Fusion===
Line 5,191: Line 4,885:


Command: ''module load SWIG''
Command: ''module load SWIG''
===Salmon===
Homepage: https://github.com/COMBINE-lab/salmon
Description: Salmon is a wicked-fast program to produce a highly-accurate,transcript-level quantification estimates from RNA-seq data.
Available versions: 0.5.1-intel-2015b-Python-2.7.10, 0.7.2-intel-2015b-Python-2.7.10, 0.8.2-foss-2016b-Python-2.7.12, 0.9.1-foss-2016b-Python-2.7.12
Command: ''module load Salmon''


===ScientificPython===
===ScientificPython===
Line 5,331: Line 5,015:


Command: ''module load Tar''
Command: ''module load Tar''
===Tcl===
Homepage: http://www.tcl.tk/
Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamicprogramming language, suitable for a very wide range of uses, including weband desktop applications, networking, administration, testing and many more.
Available versions: 8.5.12-goolf-1.4.10, 8.5.16-intel-2016a, 8.6.3-foss-2015b, 8.6.3-goolf-1.7.20, 8.6.3-intel-2015b, 8.6.4-foss-2015b, 8.6.4-foss-2016a, 8.6.4-foss-2016b, 8.6.4-goolf-1.7.20, 8.6.4-intel-2015b, 8.6.4-intel-2016a, 8.6.5-foss-2016a, 8.6.5-foss-2016b, 8.6.5-intel-2015b, 8.6.5-intel-2016a, 8.6.6-GCCcore-6.3.0, 8.6.4-goolf-1.4.10, 8.6.5-intel-2017a, 8.6.8-GCCcore-6.4.0, 8.6.7-GCCcore-6.4.0, 8.6.6-GCCcore-5.4.0, 8.6.7-GCCcore-5.4.0, 8.6.8-GCCcore-5.4.0
Command: ''module load Tcl''


===Tk===
===Tk===
Line 5,381: Line 5,055:


Command: ''module load tabix''
Command: ''module load tabix''
===tbb===
Homepage: https://01.org/tbb/
Description: Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs thattake full advantage of multicore performance, that are portable, composable and have future-proof scalability.
Available versions: 2017_U6-intel-2017a, 2017_U5-intel-2017a, 2017_U6-intel-2016a, 2017_U5-foss-2016b
Command: ''module load tbb''


===tcsh===
===tcsh===
Line 5,445: Line 5,109:


Command: ''module load torque''
Command: ''module load torque''
===util-linux===
Homepage: http://www.kernel.org/pub/linux/utils/util-linux
Description: Set of Linux utilities
Available versions: 2.26.1-intel-2015b, 2.27.1-foss-2016a, 2.28-foss-2016a, 2.28-intel-2016a, 2.29.2-intel-2017a, 2.30.1-GCCcore-6.3.0, 2.31-GCCcore-6.4.0, 2.31.1-GCCcore-6.4.0, 2.31.1-GCCcore-5.4.0
Command: ''module load util-linux''


===unblur===
===unblur===
Line 5,547: Line 5,201:


Command: ''module load rc/xget''
Command: ''module load rc/xget''
===X11===
Homepage: https://www.x.org
Description: The X Window System (X11) is a windowing system for bitmap displays
Available versions: 20160819-foss-2016b, 20160819-intel-2015b, 20160819-intel-2016a, 20170314-GCCcore-6.3.0, 20171023-GCCcore-6.4.0, 20180131-GCCcore-6.4.0, 20180131-GCCcore-5.4.0
Command: ''module load X11''


===XKeyboardConfig===
===XKeyboardConfig===
Line 5,563: Line 5,207:


Command: ''module load XKeyboardConfig''
Command: ''module load XKeyboardConfig''
===XML-Parser===
Homepage: http://search.cpan.org/~toddr/XML-Parser-2.41/
Description: This is a Perl extension interface to James Clark's XML parser, expat.
Available versions: 2.44-intel-2016a-Perl-5.22.1, 2.44_01-intel-2017a-Perl-5.24.1, 2.44_01-GCCcore-6.4.0-Perl-5.26.0, 2.44_01-GCCcore-6.4.0-Perl-5.26.1, 2.44_01-GCCcore-5.4.0-Perl-5.26.1, 2.44_01-GCCcore-5.4.0-Perl-5.24.0
Command: ''module load XML-Parser''


===xbitmaps===
===xbitmaps===
Line 5,717: Line 5,351:


Command: ''module load Yasm''
Command: ''module load Yasm''
===ZeroMQ===
Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a
Command: ''module load ZeroMQ''


===zlib===
===zlib===
Line 5,730: Line 5,358:
Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.
Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.


Available versions: 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a
Available versions: 1.2.10, 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a


Command: ''module load zlib''
Command: ''module load zlib''
===ZeroMQ===
Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a
Command: ''module load ZeroMQ''




Latest revision as of 17:02, 13 June 2019

This page shows a list of installed modules on the Cheaha research computing system. If you don't find a particular package listed on this page, please send a request to cheaha support to request the software.

This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the module avail command for the official list of software modules installed on Cheaha.

Last Update: 2019-06-13

Contents: | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

A

Name Latest version
anvio 3
atom 1.30.0
AFNI 18.2.05-intel-2016a-Python-2.7.11
ANTs 2.1.0rc3-foss-2016a
APBS 1.4-linux-static-x86_64
ASHS 2.0.0_07202018
ATK 2.26.0-intel-2017a
ATLAS 3.10.1-gompi-1.5.12-LAPACK-3.4.2
Amber 14-intel-2016a-AmberTools-15-patchlevel-13-13
Anaconda2 4.2.0
Aspera-Connect 3.6.1
AutoDock_Vina 1.1.2_linux_x86
Autoconf 2.69-GCCcore-5.4.0
annovar 2016Feb01-foss-2015b-Perl-5.22.1
ant 1.9.7-Java-1.8.0_92
ABySS 2.0.2-foss-2016a
Anaconda3 5.3.0
aaf-phylogeny 20160831
acml gcc/mp/fma4/5.3.1

B

Name Latest version
BrainSuite 15b
basespace-cli 0.8.12
brainstorm 180709
BEDTools 2.26.0-foss-2016a
BSMAP 2.90-foss-2016a
BWA 0.7.13-intel-2016a
BXH_XCEDE_TOOLS 1.11.1
BamTools 2.4.0-intel-2016a
Bismark 0.19.0-foss-2016a
Bowtie 1.1.2-foss-2016a
Bowtie2 2.3.3-intel-2017a
BreakDancer 1.4.5-intel-2016a
BCFtools 1.6-intel-2016a
BLAST+ 2.6.0-intel-2017a-Python-2.7.13
Biopython 1.70-intel-2017a-Python-3.6.1
bioitx jupyter
blacs openmpi/gcc/64/1.1patch03
blas gcc/64/3.8.0
bonnie++ 1.97.3

C

Name Latest version
cmg 2016.101.GU
cytoscape 2.8.2
cellranger 2.2.0
crossmap 0.2.8
chezscheme 9.5
ceres 1.13.0
CBLAS 20110120-foss-2016b
CD-HIT 4.6.8-intel-2017a
CHARMM 40b1-intel-2016a
CHASE v1
CUDA 9.2.88-GCC-7.3.0-2.30
Circos 0.69-5-intel-2016a-Perl-5.18.2
ConnectomeWorkbench 1.3.1
Cufflinks 2.2.1-goolf-1.7.20
cairo 1.14.12-GCCcore-6.4.0
configurable-http-proxy 1.3.0-foss-2016a-nodejs-4.4.7
cutadapt 1.12
CTFFIND 4.1.8-foss-2016b
cuDNN 7.0.5-CUDA-9.0.176
ctffind 4.0.17-foss-2016b
cluster-tools-dell 8.1
cluster-tools 8.1
cuda90 toolkit/9.0.176
cuda91 toolkit/9.1.85
cuda80 toolkit/8.0.61
cuda10.0 toolkit/10.0.130
cuda92 toolkit/9.2.88

D

Name Latest version
delly 0.7.6
dsistudio dsistudio-20151020
detonate 1.11
dicombrowser 1.7.0b5
drracket 7.1
DBus 1.11.20-intel-2017a
DMTCP 2.5.0
Doxygen 1.8.13-GCCcore-6.4.0
damageproto 1.2.1-intel-2016a
dbus-glib 0.108-intel-2017a
DB 6.2.32-intel-2017a
dvctools recommended

E

Name Latest version
EMAN2 2.2
EIGENSOFT 6.1.4-foss-2016b
ENT 1.0.2
EPACTS 3.2.6-foss-2016b
Elk 4.3.6-intel-2016a
Emacs 24.5-GCC-4.9.3-2.25
entrypoints 0.2.2-foss-2016a-Python-3.5.1
eudev 3.1.5-foss-2016b
EDGE_pro 1.3.1
exonerate 2.2.0
EDGE_pro_patch 1.3.1-2

F

Name Latest version
FSL 6.0.0
fdtd 8.17.1157-1
freesurfer Dev/10_29_16
fpart 1.1.0
freeimage 3.18
FASTX-Toolkit 0.0.14-intel-2015b
FIAT 1.6.0-intel-2015b-Python-2.7.11
FLTK 1.3.3-foss-2016b
FLUENT 19.1
FSL 5.0.10-intel-2017a
FastQC 0.11.7-Java-1.8.0_74
FastTree 2.1.9-goolf-1.4.10
FreeSurfer 6.0.0-centos6_x86_64
fastPHASE 1.4.8
file 5.28-foss-2016b
fixesproto 5.0-foss-2016a
flex 2.6.3-GCCcore-7.3.0
fontsproto 2.1.3-intel-2016a
freeglut 3.0.0-intel-2017a
FastQ_Screen 0.11.2
Firefox 44.0.2
FreeXL 1.0.2-intel-2016a
freebayes 1.1.0-goolf-1.7.20_39e5e4b
frealign 9.11-intel-2016a-avx-mp
FriBidi 1.0.1-foss-2016b
freeipmi 1.5.7
fftw2 openmpi/gcc/64/float/2.1.5
fftw3 openmpi/gcc/64/3.3.7

G

Name Latest version
GEMMA GEMMA_Rec
gromacs-intel 2018.1
GeneTorrent GeneTorrent_4.0.0-9
GATK 3.7-Java-1.8.0_92
GC3Pie 2.4.2
GCC 7.3.0-2.30
GCCcore 7.3.0
GD 2.52-intel-2016a-Perl-5.18.2
GDAL 2.2.3-foss-2018a-Python-3.6.4
GNU 4.9.3-2.25
GObject-Introspection 1.48.0-foss-2016a
GTK+ 2.24.31-intel-2017a
Gdk-Pixbuf 2.36.10-intel-2017a
gawk 4.0.2-goolf-1.4.10
gcccuda 2018b
glproto 1.4.17-foss-2016b
gnuplot 5.0.3-intel-2016a
gnutls 3.4.7-GNU-4.9.3-2.25
goolf 1.7.20
grep 2.15-goolf-1.4.10
groff 1.22.2-foss-2016b
gtool 0.7.5_linux_x86_64
guile 1.8.8-GNU-4.9.3-2.25
GEOS 3.6.2-foss-2018a-Python-3.6.4
GStreamer 1.8.3-foss-2016a
GConf 3.2.6-intel-2017a
GST-plugins-base 0.10.36-intel-2017a
gdc-client 1.3.0-intel-2016a-Python-2.7.12
Gctf 1.06_devel
gzip 1.6
gcc 7.2.0
gdb 8.0.1
globalarrays openmpi/gcc/64/5.6.1

H

Name Latest version
hydrasv 0.5.3
HOMER 4.9
HAPGEN2 2.2.0
HISAT2 2.1.0-foss-2016b
HPL 2.2-intel-2016a
HTSeq 0.6.1p1-intel-2015b-Python-2.7.8
HarfBuzz 1.5.1-intel-2017a
Hypre 2.10.1-intel-2015b
h5py 2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16
help2man 1.47.4-GCCcore-5.4.0
hwloc 1.11.8
HMMER 3.1b2-intel-2016a
hdf5 1.10.1
hdf5_18 1.8.20
hpl 2.2

I

Name Latest version
intel compiler/64/ps_2016/2016.0.047
IMPUTE2 2.3.2_x86_64_static
IPython 5.0.0-foss-2016a-Python-3.5.1
icc 2016.3.210-GCC-5.4.0-2.26
iccifort 2016.3.210-GCC-5.4.0-2.26
ifort 2016.3.210-GCC-5.4.0-2.26
iimpi 2016b
imkl 11.3.3.210-iimpi-2016b
impi 5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26
inputproto 2.3.1-intel-2016a
intel mic/sdk/3.8.4
ITK 4.12.2-foss-2016b-Python-2.7.12
ICU 61.1-GCCcore-6.4.0
ipmitool 1.8.18
intel-tbb-oss intel64/2018_20180618oss
iozone 3_471

J

Name Latest version
jspr 2017-7-20
JAGS 3.4.0-goolf-1.4.10
JUnit 4.12-Java-1.8.0_92
Java .modulerc
Jellyfish 2.2.6-foss-2016b
jupyterhub 0.6.1-foss-2016a-Python-3.5.1

K

Name Latest version
Kent_tools 340
Kerberos_V5 1.12.2-intel-2015b
kbproto 1.0.7-intel-2016a
KING 2.1.2-foss-2016a
kallisto 0.43.1-intel-2017a

L

Name Latest version
lstc lsdyna
lumpy 0.2.13
lcmodel 6.3
luajit 2.0.5
libarchive 3.1.2-10
LAPACK 3.4.2-gompi-1.5.12
LeadIT 2.1.9
LibTIFF 4.0.9-GCCcore-5.4.0
Lmod 6.3-GCC-4.8.4
LocusZoom 1.3-goolf-1.7.20
Lua 5.1.4-8-GCC-4.8.4
lftp 4.6.4-GNU-4.9.3-2.25
libGLU 9.0.0-foss-2018a
libICE 1.0.9-intel-2016a
libSM 1.2.2-intel-2016a
libX11 1.6.3-intel-2016a
libXau 1.0.8-intel-2016a
libXcursor 1.1.14-foss-2016b
libXdamage 1.1.4-intel-2016a
libXdmcp 1.1.2-intel-2016a
libXext 1.3.3-intel-2016a
libXfixes 5.0.1-intel-2016a
libXfont 1.5.1-intel-2016a-freetype-2.6.3
libXft 2.3.2-foss-2016b
libXi 1.7.6-intel-2016a
libXinerama 1.1.3-foss-2016b
libXmu 1.1.2-intel-2016a
libXp 1.0.3-intel-2016a
libXpm 3.5.11-intel-2016a
libXrandr 1.5.0-intel-2016a
libXrender 0.9.9-intel-2016a
libXt 1.1.5-intel-2016a
libcerf 1.4-intel-2016a
libdrm 2.4.91-GCCcore-5.4.0
libfontenc 1.1.3-intel-2016a
libgcrypt 1.6.5-intel-2017a
libgd 2.2.4-intel-2017a
libglade 2.6.4-intel-2016a
libgpg-error 1.21-intel-2017a
libgtextutils 0.6.1-intel-2015b
libidn 1.32-GNU-4.9.3-2.25
libjpeg-turbo 1.5.3-GCCcore-5.4.0
libpciaccess 0.13.4-intel-2016a
libpthread-stubs 0.3-intel-2016a
libsodium 1.0.8-foss-2016a
libtasn1 4.7-GNU-4.9.3-2.25
libtool 2.4.6-GCCcore-5.4.0
libunistring 0.9.3-GNU-4.9.3-2.25
libxcb 1.8-foss-2016a-Python-2.7.3
libxkbcommon 0.6.1-intel-2016a
libxslt 1.1.29-intel-2017a
libsndfile 1.0.28-GCCcore-6.4.0
libyaml 0.1.7-intel-2016a
libspatialindex 1.8.5-intel-2016a
libspatialite 4.3.0a-intel-2016a
LoFreq 2.1.2-intel-2017a-Python-2.7.12
LibUUID 1.0.3-foss-2016a
LAME 3.99.5-foss-2016b
LZO 2.10-foss-2016b
libgeotiff 1.4.2-foss-2018a
lua 5.3.4
lapack gcc/64/3.8.0

M

Name Latest version
MEGA2 4.9.1
Mathematica 10.3
manta 1.0.3
mat test
matlab R2019a
metasv 0.5.2
mriconvert 2.0.8
maskface 12272017
M4 1.4.18-GCCcore-5.4.0
MACH 1.0.18
MACS 1.4.2-1-goolf-1.7.20-Python-2.7.5
MOSAIK 2.2.28-intel-2016a-20140425-24cf06
MPICH 3.0.4-GCC-4.8.1
MRIcroGL 09302016
MRIcron 06_22_15
MRtrix 0.3.16-intel-2016a-Python-2.7.11
MUSCLE 3.8.31-intel-2016a
MVAPICH2 2.2b-GCC-4.9.3-2.25
Maq 0.7.0
Mathematica 11.0.1
Maven 3.3.9
Mercurial 3.2.4-foss-2015b-Python-2.7.9
Mesa 11.1.2-foss-2016b
Minimac2 2014.9.15-intel-2015b
Minimac3 1.0.10-intel-2015b
makedepend 1.0.5-foss-2016b
matplotlib 1.5.1-foss-2016a-Python-2.7.11
motif 2.3.7-intel-2016a
MACS2 2.1.1.20160309-foss-2016a-Python-2.7.11
MEME 4.12.0-foss-2016a
MultiQC 0.8~
Mono 5.2.0.224-intel-2017a
MaSuRCA 3.2.6-foss-2018a
minimap2 2.0rc1-foss-2016b
MotionCor2 1.0.5
mpich ge/gcc/64/3.2.1
mpiexec 0.84_432
mvapich2 gcc/64/2.3b

N

Name Latest version
NAMD 2.13b2-gpu
nccl 1.3.4-1
ncdu 1.13-20.1
nighres 1.1.0b1
NASM 2.13.03-GCCcore-5.4.0
NGS 1.2.5-foss-2016b
ncbi-vdb 2.7.0-foss-2016b
netCDF 4.6.0-foss-2018a
nodejs 4.4.7-foss-2016a
numactl 2.0.11-GCCcore-7.3.0
numpy 1.10.1-goolf-1.7.20-Python-2.7.11
NLopt 2.4.2-foss-2018a
NiBabel 2.1.0-intel-2017a-Python-2.7.13
ngmlr 0.2.6-foss-2016b
NCBI-Toolkit 18.0.0-intel-2017a
NCCL 2.2.13-CUDA-8.0.61
netcdf gcc/64/4.5.0
netperf 2.7.0

O

Name Latest version
openscenegraph 3.2.1
OTF 1.12.4-gompi-1.5.12
OpenPGM 5.2.122-intel-2015b
OpenSSL 1.0.2h-foss-2016b
OpenMM 6.3-intel-2016a-Python-2.7.11
openmpi gcc/64/1.10.7
openblas dynamic/0.2.20

P

Name Latest version
parsync 1.69
PCRE 8.41-GCCcore-5.4.0
PDT 3.20-goolf-1.7.20
PETSc 3.6.3-intel-2015b-Python-2.7.11
PGI 18.5-GCC-6.4.0-2.28
PHASE 2.1.1
PIL 1.1.7-intel-2016a-Python-2.7.11
PROJ 5.0.0-foss-2018a
Pango 1.40.12-intel-2017a
Pindel 0.2.5b8-foss-2016b
ProbABEL 0.5.0
PyCairo 1.10.0-intel-2016a-Python-2.7.11
PyGObject 2.28.6-intel-2016a-Python-2.7.11
PyGTK 2.24.0-intel-2016a-Python-2.7.11
PyQt 4.11.4-intel-2016a-Python-2.7.11
PyZMQ 15.3.0-foss-2016a-Python-3.5.1-zmq4
Pygments 2.0.2-intel-2015b-Python-2.7.9
Pysam 0.9.1.4-foss-2016b-Python-2.7.12
p11-kit 0.23.2-GNU-4.9.3-2.25
parallel 20150822-GCC-4.9.2
path.py 8.2.1-foss-2016a-Python-3.5.1
perl-app-cpanminus 1.7039
pixman 0.34.0-GCCcore-5.4.0
pkgconfig 1.1.0-intel-2016a-Python-2.7.11
printproto 1.0.5-intel-2016a
prompt-toolkit 1.0.3-foss-2016a-Python-3.5.1
pysqlite 2.6.3-intel-2015b-Python-2.7.9
protobuf 3.3.0-intel-2017a
protobuf-python 3.3.0-intel-2017a-Python-3.6.1
PyYAML 3.12-intel-2016a-Python-3.5.1
prodigal 2.6.2-GCC-4.9.3-binutils-2.25
Pillow 4.3.0-intel-2017a-Python-2.7.13
p7zip 9.38.1
patchelf 0.9-foss-2016b
PCRE2 10.31-foss-2018a

Q

Name Latest version
qdirstat 1.4
Qt 4.8.7-intel-2016a
Qwt 6.1.3-intel-2016a
QwtPolar 1.1.1-intel-2016a
QUAST 4.6.3-foss-2016a-Python-2.7.11
QIIME qiime-dependencies
QWRAP v3

R

Name Latest version
RStudio 1.0.44
relion 2.1
rserver 3.5.2_X11
R DESeq2.R-3.4.3-intel-2017a-X11-20170314
RAxML 8.1.1-goolf-1.4.10-mt-avx
RSeQC 2.6.3-goolf-1.7.20-Python-2.7.10-R-3.2.1
Ruby 2.3.3
randrproto 1.5.0-intel-2016a
renderproto 0.11-intel-2016a
requests 2.7.0-intel-2015b-Python-2.7.9
ResMap 1.1.4
RELION 2.1-intel-2016a-CUDA-8.0.44
Rust 1.30.1-foss-2016b

S

Name Latest version
snakemakeslurm_local 4.8.0-1
SAS v9.4
Salmon 0.7.2
soapsv 1.3
snakemake 4.8.0
sublime_text 3
S.A.G.E. 6.3
SCOTCH 6.0.4-intel-2015b
SHRiMP 2.2.3-goolf-1.4.10
SIP 4.18-intel-2016a-Python-2.7.11
SOLAR-Eclipse 8.1.1
SPAdes 3.12.0-foss-2016b
SPPARKS 07192016-intel-2016a
STAR-Fusion 0.8.0-goolf-1.4.10-Perl-5.16.3
STAR 2.5.2b~
SWIG 3.0.12-foss-2018a-Python-2.7.14
ScientificPython 2.9.4-intel-2015b-Python-2.7.11
Spack 0.10.0
scipy 0.17.0-intel-2016a-Python-2.7.11
shapeit 2.r837.GLIBCv2.12_linux_x86_64
sympy 0.7.6.1-intel-2015b-Python-2.7.11
SRA-Toolkit 2.8.2-1-centos_linux64
sparsehash 2.0.2-foss-2016a
Spark 2.2.0-Hadoop-2.6-Java-1.8.0_144
summovie 1.0.2
snakemakeslurm 4.8.0-1
scalapack openmpi/gcc/64/2.0.2
sge 2011.11p1
slurm 17.11.8

T

Name Latest version
tortoise 3.1.2
transdecoder 5.3.0
torch 7
tarquin 4.3.10
tcllib 1.19
Tar 1.29-goolf-1.4.10
Tk 8.6.8-foss-2018a
TopHat 2.1.1-foss-2016a
Trim_Galore 0.4.4-foss-2016b
Trimmomatic 0.36-Java-1.8.0_92
Trinity 2.2.0-foss-2016a
tabix 0.2.6-intel-2015b
tcsh 6.19.00-intel-2016a
testpath 0.3-foss-2016a-Python-3.5.1
texinfo 6.4-GCCcore-5.4.0
Tensorflow 1.2.0-intel-2017a-Python-3.6.1
TransDecoder 5.1.0-intel-2017a-Perl-5.24.1
trim_galore 0.4.2~
torque 6.1.1

U

Name Latest version
unblur 1.0.2
usearch 7.0.1090

V

Name Latest version
vmd 1.9.3
VEGAS 0.8.27
VICUNA 1.3
VPhaser-2 02112013-intel-2016a
VTK 6.3.0-foss-2016b-Python-2.7.12
VCFtools 0.1.15-intel-2016a-Perl-5.22.1

W

Name Latest version
wcwidth 0.1.7-foss-2016a-Python-3.5.1
wxPython 3.0.2.0-intel-2017a-Python-2.7.13
wxWidgets 3.0.3-foss-2016b

X

Name Latest version
xget xget-public
XKeyboardConfig 2.17-intel-2016a
xbitmaps 1.1.1-intel-2016a
xcb-proto 1.7-foss-2016a-Python-2.7.3
xcb-util-image 0.4.0-intel-2016a
xcb-util-keysyms 0.4.0-intel-2016a
xcb-util-renderutil 0.3.9-intel-2016a
xcb-util-wm 0.4.1-intel-2016a
xcb-util 0.4.0-intel-2016a
xextproto 7.3.0-intel-2016a
xf86vidmodeproto 2.3.1-intel-2016a
xineramaproto 1.2.1-foss-2016b
xorg-macros 1.19.0-intel-2016a
xprop 1.2.2-foss-2016b
xproto 7.0.28-intel-2016a
xtrans 1.3.5-intel-2016a
Xerces-C++ 3.1.2-intel-2015b
XQilla 2.3.2-intel-2015b
x264 20160614-foss-2016b
x265 2.4-foss-2016b

Y

Name Latest version
Yasm 1.3.0-foss-2016b

Z

Name Latest version
zlib 1.2.9-intel-2017a
ZeroMQ 4.1.4-foss-2016a

Software Detail

anvio

Available versions: 3

Command: module load rc/anvio

atom

Available versions: 1.30.0

Command: module load rc/atom

AFNI

Homepage: http://afni.nimh.nih.gov/

Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data -a technique for mapping human brain activity.

Available versions: 17.1.08-intel-2016a-Python-2.7.11, dev-intel-2016a-Python-2.7.11, linux_openmp_64-goolf-1.7.20-20160616, 18.2.05-intel-2016a-Python-2.7.11

Command: module load AFNI

ANTs

Available versions: 2.1.0rc3-foss-2016a

Command: module load ANTs

APBS

Available versions: 1.4-linux-static-x86_64

Command: module load APBS

ASHS

Homepage: https://sites.google.com/site/hipposubfields/home

Description: Automatic Segmentation of Hippocampal Subfields (ASHS)

Available versions: rev103_20140612, 2.0.0_07202018

Command: module load ASHS

ATK

Homepage: https://developer.gnome.org/ATK/stable/

Description: ATK provides the set of accessibility interfaces that are implemented by othertoolkits and applications. Using the ATK interfaces, accessibility tools havefull access to view and control running applications.

Available versions: 2.18.0-intel-2016a, 2.26.0-intel-2017a

Command: module load ATK

ATLAS

Available versions: 3.10.1-gompi-1.5.12-LAPACK-3.4.2

Command: module load ATLAS

Amber

Available versions: 14-intel-2016a-AmberTools-15-patchlevel-13-13

Command: module load Amber

Anaconda2

Homepage: https://www.continuum.io/anaconda-overview}

Available versions: 4.0.0, 4.2.0

Command: module load Anaconda2

Aspera-Connect

Available versions: 3.6.1

Command: module load Aspera-Connect

AutoDock_Vina

Available versions: 1.1.2_linux_x86

Command: module load AutoDock_Vina

Autoconf

Homepage: http://www.gnu.org/software/autoconf/

Description: Autoconf is an extensible package of M4 macros that produce shell scriptsto automatically configure software source code packages. These scripts can adapt thepackages to many kinds of UNIX-like systems without manual user intervention. Autoconfcreates a configuration script for a package from a template file that lists theoperating system features that the package can use, in the form of M4 macro calls.

Available versions: 2.69, 2.69-GCC-4.8.4, 2.69-GCC-4.9.3-2.25, 2.69-GNU-4.9.3-2.25, 2.69-foss-2016a, 2.69-foss-2016b, 2.69-goolf-1.7.20, 2.69-intel-2015b, 2.69-intel-2016a, 2.69-GCCcore-6.3.0, 2.69-GCC-5.4.0-2.26, 2.69-intel-2017a, 2.69-GCCcore-6.4.0, 2.69-GCCcore-7.3.0, 2.69-GCCcore-5.4.0

Command: module load Autoconf

annovar

Available versions: 2016Feb01-foss-2015b-Perl-5.22.1

Command: module load annovar

ant

Available versions: 1.9.6-Java-1.7.0_80, 1.9.7-Java-1.8.0_92

Command: module load ant

ABySS

Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Available versions: 1.9.0-foss-2016a, 2.0.2-foss-2016a

Command: module load ABySS

Anaconda3

Homepage: https://www.continuum.io/anaconda-overview

Description: Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platformthat empowers companies to adopt a modern open data science analytics architecture.

Available versions: 4.4.0, 5.0.1, 5.2.0, 5.1.0, 5.3.0

Command: module load Anaconda3

aaf-phylogeny

Available versions: 20160831

Command: module load aaf-phylogeny

acml

Available versions: gcc-int64/64/5.3.1, gcc-int64/fma4/5.3.1, gcc-int64/mp/64/5.3.1, gcc-int64/mp/fma4/5.3.1, gcc/64/5.3.1, gcc/fma4/5.3.1, gcc/mp/64/5.3.1, gcc/mp/fma4/5.3.1

Command: module load acml

BrainSuite

Available versions: 15b

Command: module load rc/BrainSuite

basespace-cli

Available versions: 0.8.12

Command: module load rc/basespace-cli

brainstorm

Available versions: 180709

Command: module load rc/brainstorm

BEDTools

Available versions: 2.26.0-foss-2016a

Command: module load BEDTools

BSMAP

Available versions: 2.90-foss-2016a

Command: module load BSMAP

BWA

Available versions: 0.7.13-intel-2015b, 0.7.13-intel-2016a

Command: module load BWA

BXH_XCEDE_TOOLS

Available versions: 1.11.1

Command: module load BXH_XCEDE_TOOLS

BamTools

Available versions: 2.4.0-goolf-1.7.20, 2.4.0-intel-2016a

Command: module load BamTools

Bismark

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

Description: A tool to map bisulfite converted sequence reads anddetermine cytosine methylation states

Available versions: 0.10.1-goolf-1.4.10, 0.18.0-foss-2016a, 0.18.0-goolf-1.4.10, 0.19.0-foss-2016a

Command: module load Bismark

Bowtie

Homepage: http://bowtie-bio.sourceforge.net/index.shtml}

Available versions: 1.1.1-goolf-1.4.10, 1.1.2-foss-2016a

Command: module load Bowtie

Bowtie2

Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing readsto long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000sof characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Available versions: 2.0.2-foss-2016a, 2.0.2-goolf-1.4.10, 2.2.5-goolf-1.7.20, 2.2.6-intel-2015b, 2.2.8-foss-2016a, 2.3.3-intel-2017a

Command: module load Bowtie2

BreakDancer

Available versions: 1.4.5-intel-2016a

Command: module load BreakDancer

BCFtools

Homepage: http://www.htslib.org/

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data.BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequencevariants

Available versions: 1.3.1-goolf-1.7.20, 1.6-intel-2016a

Command: module load BCFtools

BLAST+

Homepage: http://blast.ncbi.nlm.nih.gov/

Description: Basic Local Alignment Search Tool, or BLAST, is an algorithmfor comparing primary biological sequence information, such as the amino-acidsequences of different proteins or the nucleotides of DNA sequences.

Available versions: 2.6.0-intel-2017a-Python-2.7.13

Command: module load BLAST+

Biopython

Homepage: http://www.biopython.org

Description: Biopython is a set of freely available tools for biological computation writtenin Python by an international team of developers. It is a distributed collaborative effort todevelop Python libraries and applications which address the needs of current and future work inbioinformatics.

Available versions: 1.70-intel-2017a-Python-3.6.1

Command: module load Biopython

bioitx

Available versions: jupyter-0.7, jupyter-0.8, jupyter-1.0, jupyter

Command: module load bioitx

blacs

Available versions: openmpi/gcc/64/1.1patch03

Command: module load blacs

blas

Available versions: gcc/64/3.8.0

Command: module load blas

bonnie++

Available versions: 1.97.3

Command: module load bonnie++

cmg

Available versions: 2012.116.G, 2016.101.GU

Command: module load rc/cmg

cytoscape

Available versions: 2.8.2

Command: module load rc/cytoscape

cellranger

Available versions: 2.1.1, 2.2.0

Command: module load rc/cellranger

crossmap

Available versions: 0.2.8

Command: module load rc/crossmap

chezscheme

Available versions: 9.5

Command: module load rc/chezscheme

ceres

Available versions: 1.14.0, 1.13.0

Command: module load rc/ceres

CBLAS

Available versions: 20110120-foss-2016b

Command: module load CBLAS

CD-HIT

Homepage: http://weizhong-lab.ucsd.edu/cd-hit/

Description: CD-HIT is a very widely used program for clustering andcomparing protein or nucleotide sequences.

Available versions: 4.6.4-foss-2015b-2015-0603, 4.6.6-foss-2016b, 4.6.8-intel-2017a

Command: module load CD-HIT

CHARMM

Available versions: 40b1-intel-2016a

Command: module load CHARMM

CHASE

Available versions: v1

Command: module load CHASE

CUDA

Homepage: https://developer.nvidia.com/cuda-toolkit

Description: CUDA (formerly Compute Unified Device Architecture) is a parallelcomputing platform and programming model created by NVIDIA and implemented by thegraphics processing units (GPUs) that they produce. CUDA gives developers accessto the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

Available versions: 7.5.18, 8.0.61_375.26-GCC-5.4.0-2.26, 8.0.61, 8.0.44, 9.2.148.1, 9.0.176, 9.2.88-GCC-7.3.0-2.30

Command: module load CUDA

Circos

Available versions: 0.69-5-intel-2016a-Perl-5.18.2

Command: module load Circos

ConnectomeWorkbench

Homepage: http://www.humanconnectome.org/software/connectome-workbench.html

Description: Connectome Workbench is an open-sourcevisualization and discovery tool used to explore data generatedby the Human Connectome Project. The distribution includes wb_view,a GUI-based visualization platform, and wb_command, a command-lineprogram for performing a variety of algorithmic tasks using volume,surface, and grayordinate data.

Available versions: 1.2.2, 1.3.1

Command: module load ConnectomeWorkbench

Cufflinks

Available versions: 2.2.1-foss-2016a, 2.2.1-goolf-1.7.20

Command: module load Cufflinks

cairo

Homepage: http://cairographics.org

Description: Cairo is a 2D graphics library with support for multiple output devices.Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

Available versions: 1.14.6-intel-2015b, 1.14.6-intel-2016a, 1.14.6-intel-2016a-GLib-2.48.0, 1.14.8-intel-2017a, 1.14.10-GCCcore-6.3.0, 1.14.6-foss-2016b, 1.14.6-foss-2016b-GLib-2.48.0, 1.14.6-foss-2016a-GLib-2.48.0, 1.14.12-GCCcore-6.4.0

Command: module load cairo

configurable-http-proxy

Available versions: 1.3.0-foss-2016a-nodejs-4.4.7

Command: module load configurable-http-proxy

cutadapt

Available versions: 1.14-foss-2016b-Python-2.7.12, 1.9.1-foss-2016b-Python-2.7.12, 1.12

Command: module load cutadapt

CTFFIND

Homepage: http://grigoriefflab.janelia.org/ctf

Description: CTFFIND4 is a program for finding CTFs of electron micrographs.

Available versions: 4.1.8-intel-2016a, 4.1.8-foss-2016b

Command: module load CTFFIND

cuDNN

Homepage: https://developer.nvidia.com/cudnn

Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives fordeep neural networks.

Available versions: 6.0-CUDA-8.0.61, 5.1-CUDA-8.0.61, 7.0.5-CUDA-9.0.176

Command: module load cuDNN

ctffind

Homepage: http://grigoriefflab.janelia.org/ctffind4

Description: program for finding CTFs of electron micrographs

Available versions: 4.0.17-foss-2016b

Command: module load ctffind

cluster-tools-dell

Available versions: 8.1

Command: module load cluster-tools-dell

cluster-tools

Available versions: 8.1

Command: module load cluster-tools

cuda90

Available versions: blas/9.0.176, fft/9.0.176, nsight/9.0.176, profiler/9.0.176, toolkit/9.0.176

Command: module load cuda90

cuda91

Available versions: blas/9.1.85, fft/9.1.85, nsight/9.1.85, profiler/9.1.85, toolkit/9.1.85

Command: module load cuda91

cuda80

Available versions: blas/8.0.61, fft/8.0.61, nsight/8.0.61, profiler/8.0.61, toolkit/8.0.61

Command: module load cuda80

cuda10.0

Available versions: blas/10.0.130, fft/10.0.130, nsight/10.0.130, profiler/10.0.130, toolkit/10.0.130

Command: module load cuda10.0

cuda92

Available versions: blas/9.2.88, fft/9.2.88, nsight/9.2.88, profiler/9.2.88, toolkit/9.2.88

Command: module load cuda92

delly

Available versions: 0.7.6

Command: module load rc/delly

dsistudio

Available versions: dsistudio-20151020

Command: module load rc/dsistudio

detonate

Available versions: 1.11

Command: module load rc/detonate

dicombrowser

Available versions: 1.7.0b5

Command: module load rc/dicombrowser

drracket

Available versions: 7.1

Command: module load rc/drracket

DBus

Homepage: http://dbus.freedesktop.org/doc/dbus-glib

Description: D-Bus is a message bus system, a simple way for applications to talkto one another. In addition to interprocess communication, D-Bus helpscoordinate process lifecycle; it makes it simple and reliable to codea "single instance" application or daemon, and to launch applicationsand daemons on demand when their services are needed.

Available versions: 1.10.8-intel-2016a, 1.11.20-intel-2017a

Command: module load DBus

DMTCP

Available versions: 2.4.5, 2.5.0

Command: module load DMTCP

Doxygen

Homepage: http://www.doxygen.org

Description: Doxygen is a documentation system for C++, C, Java, Objective-C, Python,IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to someextent D.

Available versions: 1.8.11-foss-2016a, 1.8.11-foss-2016b, 1.8.11-intel-2015b, 1.8.11-intel-2016a, 1.8.13-GCCcore-6.3.0, 1.8.13-GCCcore-6.4.0

Command: module load Doxygen

damageproto

Available versions: 1.2.1-foss-2016b, 1.2.1-goolf-1.7.20, 1.2.1-intel-2016a

Command: module load damageproto

dbus-glib

Homepage: http://dbus.freedesktop.org/doc/dbus-glib

Description: D-Bus is a message bus system, a simple way for applications to talk to one another.

Available versions: 0.106-intel-2016a, 0.108-intel-2017a

Command: module load dbus-glib

DB

Homepage: http://www.oracle.com/technetwork/products/berkeleydb

Description: Berkeley DB enables the development of custom data management solutions,without the overhead traditionally associated with such custom projects.

Available versions: 6.0.30-foss-2016a, 6.2.32-intel-2017a

Command: module load DB

dvctools

Available versions: 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.2, 1.0, latest, recommended

Command: module load dvctools

EMAN2

Available versions: 2.2

Command: module load rc/EMAN2

EIGENSOFT

Homepage: http://www.hsph.harvard.edu/alkes-price/software/

Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al.2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principalcomponents analysis to explicitly model ancestry differences between cases and controls along continuous axes ofvariation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestralpopulations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFTpackage has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

Available versions: 6.1.1-goolf-1.7.20, 6.1.4-foss-2016b

Command: module load EIGENSOFT

ENT

Available versions: 1.0.2

Command: module load ENT

EPACTS

Available versions: 3.2.6-foss-2016b

Command: module load EPACTS

Elk

Homepage: http://elk.sourceforge.net/}

Available versions: 4.0.15-intel-2016a, 4.3.6-intel-2016a

Command: module load Elk

Emacs

Available versions: 24.5-GCC-4.9.3-2.25

Command: module load Emacs

entrypoints

Available versions: 0.2.2-foss-2016a-Python-3.5.1

Command: module load entrypoints

eudev

Homepage: https://wiki.gentoo.org/wiki/Project:Eudev

Description: eudev is a fork of systemd-udev with the goal of obtainingbetter compatibility with existing software such asOpenRC and Upstart, older kernels, various toolchainsand anything else required by users and various distributions.

Available versions: 3.1.5-goolf-1.7.20, 3.1.5-intel-2016a, 3.1.5-foss-2016b

Command: module load eudev

EDGE_pro

Homepage: http://ccb.jhu.edu/software/EDGE-pro/

Description: EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes)is an efficient software system to estimate gene expression levels inprokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignmentand then estimates expression directly from the alignment results.

Available versions: 1.3.1

Command: module load EDGE_pro

exonerate

Available versions: 2.2.0

Command: module load exonerate

EDGE_pro_patch

Homepage: http://ccb.jhu.edu/software/EDGE-pro/

Description: EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes)is an efficient software system to estimate gene expression levels inprokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignmentand then estimates expression directly from the alignment results.

Available versions: 1.3.1-2

Command: module load EDGE_pro_patch

FSL

Homepage: http://www.fmrib.ox.ac.uk/fsl/

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Available versions: 5.0.9-Modified-fsl_sub, 6.0.0

Command: module load rc/FSL

fdtd

Available versions: 8.17.1157-1

Command: module load rc/fdtd

freesurfer

Available versions: freesurfer-5.3.0, freesurfer-5.3.0-HCP, Dev/10_29_16

Command: module load rc/freesurfer

fpart

Available versions: 1.1.0

Command: module load rc/fpart

freeimage

Available versions: 3.18

Command: module load rc/freeimage

FASTX-Toolkit

Available versions: 0.0.14-intel-2015b

Command: module load FASTX-Toolkit

FIAT

Available versions: 1.6.0-intel-2015b-Python-2.7.11

Command: module load FIAT

FLTK

Homepage: http://www.fltk.org

Description: FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows,and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGLand its built-in GLUT emulation.

Available versions: 1.3.3-intel-2016a, 1.3.3-foss-2016b

Command: module load FLTK

FLUENT

Homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent

Description: ANSYS FLUENT software contains the broad physical modeling capabilities neededto model flow, turbulence, heat transfer, and reactions for industrial applications ranging fromair flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms,from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

Available versions: 18.0, 19.1

Command: module load FLUENT

FSL

Homepage: http://www.fmrib.ox.ac.uk/fsl/

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Available versions: 5.0.9-centos6_64, 6.0.0-intel-2017a, 5.0.10-intel-2017a

Command: module load FSL

FastQC

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Description: FastQC is a quality control application for high throughput sequence data.It reads in sequence data in a variety of formats and can either provide an interactiveapplication to review the results of several different QC checks, or create an HTML basedreport which can be integrated into a pipeline.

Available versions: 0.11.5-Java-1.7.0_80, 0.11.5-Java-1.8.0_74, 0.11.7-Java-1.8.0_74

Command: module load FastQC

FastTree

Available versions: 2.1.7-goolf-1.4.10, 2.1.9-goolf-1.4.10

Command: module load FastTree

FreeSurfer

Available versions: 5.3.0-centos6_x86_64, 6.0.0-centos6_x86_64

Command: module load FreeSurfer

fastPHASE

Available versions: 1.4.8

Command: module load fastPHASE

file

Available versions: 5.28-foss-2016b

Command: module load file

fixesproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X.org FixesProto protocol headers.

Available versions: 5.0-foss-2016b, 5.0-goolf-1.7.20, 5.0-intel-2015b, 5.0-intel-2016a, 5.0-foss-2016a

Command: module load fixesproto

flex

Homepage: http://flex.sourceforge.net/

Description: Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

Available versions: 2.5.35-foss-2016a, 2.5.39, 2.5.39-GCC-4.9.3-binutils-2.25, 2.5.39-GCCcore-4.9.3, 2.5.39-intel-2015b, 2.6.0, 2.6.0-GCCcore-5.4.0, 2.6.0-foss-2016a, 2.6.0-foss-2016b, 2.6.0-goolf-1.7.20, 2.6.0-intel-2015b, 2.6.0-intel-2016a, 2.6.3-GCCcore-6.3.0, 2.6.0-GCCcore-6.1.0, 2.6.4-GCCcore-6.3.0, 2.6.3, 2.6.4-GCCcore-6.4.0, 2.5.39-intel-2016a, 2.6.0-intel-2017a, 2.6.4, 2.6.4-GCCcore-7.3.0, 2.6.3-GCCcore-5.4.0, 2.6.4-GCCcore-5.4.0, 2.6.3-GCCcore-7.3.0

Command: module load flex

fontsproto

Available versions: 2.1.3-foss-2016b, 2.1.3-goolf-1.7.20, 2.1.3-intel-2016a

Command: module load fontsproto

freeglut

Homepage: http://freeglut.sourceforge.net/

Description: freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

Available versions: 3.0.0-foss-2016b, 3.0.0-intel-2016a, 3.0.0-intel-2017a

Command: module load freeglut

FastQ_Screen

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Description: FastQ Screen allows you to set up a standard set of librariesagainst which all of your sequences can be searched. Your search libraries mightcontain the genomes of all of the organisms you work on, along with PhiX,Vectors or other contaminants commonly seen in sequencing experiments.

Available versions: 0.11.2

Command: module load FastQ_Screen

Firefox

Homepage: https://www.mozilla.org/en-US/firefox/new/

Description: Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on theMozilla code base and offers customization options and features such as its capability to block pop-up windows,tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.

Available versions: 44.0.2

Command: module load Firefox

FreeXL

Homepage: https://www.gaia-gis.it/fossil/freexl/index

Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Available versions: 1.0.2-foss-2016b, 1.0.2-intel-2016a

Command: module load FreeXL

freebayes

Homepage: https://github.com/ekg/freebayes

Description: Bayesian haplotype-based polymorphism discovery and genotyping.

Available versions: 1.1.0-goolf-1.7.20_39e5e4b

Command: module load freebayes

frealign

Homepage: http://grigoriefflab.janelia.org/frealign

Description: Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images ofsingle particles.

Available versions: 9.11-intel-2016a-avx-mp

Command: module load frealign

FriBidi

Homepage: https://directory.fsf.org/wiki/Fribidi

Description: FriBidi is a free implementation of the Unicode Bidirectional (BiDi) Algorithm. It also providesutility functions to aid in the development of interactive editors and widgets that implement BiDi functionality.The BiDi algorithm is a prerequisite for supporting right-to-left scripts such as Hebrew, Arabic, Syriac, andThaana.

Available versions: 1.0.1-foss-2016b

Command: module load FriBidi

freeipmi

Available versions: 1.5.7

Command: module load freeipmi

fftw2

Available versions: openmpi/gcc/64/double/2.1.5, openmpi/gcc/64/float/2.1.5

Command: module load fftw2

fftw3

Available versions: openmpi/gcc/64/3.3.7

Command: module load fftw3

GEMMA

Available versions: GEMMA_Rec

Command: module load rc/GEMMA

gromacs-intel

Available versions: 5.1.1, 2018.1

Command: module load rc/gromacs-intel

GeneTorrent

Available versions: GeneTorrent_4.0.0-9

Command: module load rc/GeneTorrent

GATK

Available versions: 3.7-Java-1.8.0_112, 3.7-Java-1.8.0_92

Command: module load GATK

GC3Pie

Available versions: 2.4.2

Command: module load GC3Pie

GCC

Homepage: http://gcc.gnu.org/

Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,as well as libraries for these languages (libstdc++, libgcj,...).

Available versions: 4.7.2, 4.8.1, 4.8.2, 4.8.4, 4.9.2, 4.9.3, 4.9.3-2.25, 4.9.3-binutils-2.25, 5.4.0-2.26, system, 6.1.0-2.27, 6.3.0-2.27, 6.4.0-2.28, 4.4.7, 7.3.0-2.30

Command: module load GCC

GCCcore

Homepage: http://gcc.gnu.org/

Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,as well as libraries for these languages (libstdc++, libgcj,...).

Available versions: 4.9.3, 5.4.0, 6.3.0, 6.1.0, 6.4.0, 7.3.0

Command: module load GCCcore

GD

Available versions: 2.52-intel-2016a-Perl-5.18.2

Command: module load GD

GDAL

Homepage: http://www.gdal.org/

Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT styleOpen Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data modelto the calling application for all supported formats. It also comes with a variety of useful commandline utilities fordata translation and processing.

Available versions: 2.0.2-intel-2016a, 2.1.0-foss-2016a, 2.1.0-foss-2016b, 2.1.0-intel-2015b, 2.1.0-intel-2016a, 2.1.3-intel-2017a-Python-2.7.13, 2.1.3-foss-2016b-Python-2.7.12, 2.1.3-intel-2016a-Python-2.7.12, 2.2.3-foss-2018a-Python-3.6.4

Command: module load GDAL

GNU

Available versions: 4.9.3-2.25

Command: module load GNU

GObject-Introspection

Homepage: https://wiki.gnome.org/GObjectIntrospection/

Description: GObject introspection is a middleware layer between C libraries(using GObject) and language bindings. The C library can be scanned atcompile time and generate a metadata file, in addition to the actualnative C library. Then at runtime, language bindings can read thismetadata and automatically provide bindings to call into the C library.

Available versions: 1.47.1-foss-2016b, 1.47.1-intel-2016a, 1.48.0-intel-2016a, 1.53.5-intel-2017a-Python-2.7.13, 1.48.0-foss-2016b, 1.48.0-foss-2016a

Command: module load GObject-Introspection

GTK+

Homepage: https://developer.gnome.org/gtk+/stable/

Description: The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

Available versions: 2.24.28-intel-2016a, 2.24.31-intel-2017a

Command: module load GTK+

Gdk-Pixbuf

Homepage: https://developer.gnome.org/gdk-pixbuf/stable/

Description: The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation.It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past itwas distributed as part of GTK+ 2 but it was split off into a separate packagein preparation for the change to GTK+ 3.

Available versions: 2.32.3-intel-2016a, 2.36.10-intel-2017a

Command: module load Gdk-Pixbuf

gawk

Available versions: 4.0.2-goolf-1.4.10

Command: module load gawk

gcccuda

Homepage: (none)

Description: GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

Available versions: 2017.01, 2018b

Command: module load gcccuda

glproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X protocol and ancillary headers

Available versions: 1.4.17-intel-2016a, 1.4.17-foss-2016b

Command: module load glproto

gnuplot

Available versions: 5.0.3-foss-2016b, 5.0.3-intel-2016a

Command: module load gnuplot

gnutls

Available versions: 3.4.7-GNU-4.9.3-2.25

Command: module load gnutls

goolf

Available versions: 1.4.10, 1.7.20

Command: module load goolf

grep

Available versions: 2.15-goolf-1.4.10

Command: module load grep

groff

Available versions: 1.22.2, 1.22.2-foss-2016b

Command: module load groff

gtool

Available versions: 0.7.5_linux_x86_64

Command: module load gtool

guile

Available versions: 1.8.8-GNU-4.9.3-2.25

Command: module load guile

GEOS

Homepage: http://trac.osgeo.org/geos

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

Available versions: 3.6.1-intel-2017a-Python-2.7.13, 3.6.1-foss-2016b-Python-2.7.12, 3.6.1-intel-2016a-Python-2.7.12, 3.6.2-foss-2018a-Python-3.6.4

Command: module load GEOS

GStreamer

Homepage: http://gstreamer.freedesktop.org/

Description: GStreamer is a library for constructing graphs of media-handlingcomponents. The applications it supports range from simpleOgg/Vorbis playback, audio/video streaming to complex audio(mixing) and video (non-linear editing) processing.

Available versions: 0.10.36-intel-2017a, 1.8.3-foss-2016b, 1.8.3-foss-2016a

Command: module load GStreamer

GConf

Homepage: https://projects.gnome.org/gconf/

Description: GConf is a system for storing application preferences.It is intended for user preferences; not configurationof something like Apache, or arbitrary data storage.

Available versions: 3.2.6-intel-2017a

Command: module load GConf

GST-plugins-base

Homepage: http://gstreamer.freedesktop.org/

Description: GStreamer is a library for constructing graphs of media-handlingcomponents. The applications it supports range from simpleOgg/Vorbis playback, audio/video streaming to complex audio(mixing) and video (non-linear editing) processing.

Available versions: 0.10.36-intel-2017a

Command: module load GST-plugins-base

gdc-client

Homepage: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool

Description: The gdc-client provides several convenience functions over the GDC API which provides generaldownload/upload via HTTPS.

Available versions: 1.0.1-intel-2016a-Python-2.7.12, 1.3.0-intel-2016a-Python-2.7.12

Command: module load gdc-client

Gctf

Homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/

Description: Gctf is a tool for real-time CTF determination and correction.

Available versions: 1.06, 1.06_devel

Command: module load Gctf

gzip

Homepage: http://www.gnu.org/software/gzip/

Description: gzip (GNU zip) is a popular data compression program as a replacement for compress

Available versions: 1.8-GCCcore-6.3.0, 1.6

Command: module load gzip

gcc

Available versions: 7.2.0

Command: module load gcc

gdb

Available versions: 8.0.1

Command: module load gdb

globalarrays

Available versions: openmpi/gcc/64/5.6.1

Command: module load globalarrays

hydrasv

Available versions: 0.5.3

Command: module load rc/hydrasv

HOMER

Available versions: 4.9

Command: module load rc/HOMER

HAPGEN2

Available versions: 2.2.0

Command: module load HAPGEN2

HISAT2

Available versions: 2.1.0-foss-2016b

Command: module load HISAT2

HPL

Available versions: 2.1-intel-2016a, 2.2-intel-2016a

Command: module load HPL

HTSeq

Available versions: 0.6.1p1-foss-2016b-Python-2.7.12, 0.6.1p1-intel-2015b-Python-2.7.8

Command: module load HTSeq

HarfBuzz

Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz

Description: HarfBuzz is an OpenType text shaping engine.

Available versions: 1.1.3-foss-2016b, 1.1.3-intel-2016a, 1.2.7-intel-2016a, 1.5.1-intel-2017a

Command: module load HarfBuzz

Hypre

Available versions: 2.10.1-intel-2015b

Command: module load Hypre

h5py

Available versions: 2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16

Command: module load h5py

help2man

Homepage: https://www.gnu.org/software/help2man/

Description: help2man produces simple manual pages from the '--help' and '--version' output of other commands.

Available versions: 1.47.4-GCCcore-6.3.0, 1.47.4, 1.47.4-GCCcore-6.4.0, 1.47.4-GCCcore-7.3.0, 1.47.4-GCCcore-5.4.0

Command: module load help2man

hwloc

Available versions: 1.10.1-GCC-4.8.4, 1.11.0-GNU-4.9.3-2.25, 1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25, 1.11.2-GCC-4.9.3-2.25, 1.11.3-GCC-5.4.0-2.26, 1.11.5-GCC-5.4.0-2.26, 1.6.2-GCC-4.7.2, 1.8.1-GCC-4.8.2, 1.11.3-intel-2017a, 1.11.3-GCC-6.1.0-2.27, 1.11.5-GCC-6.3.0-2.27, 1.11.8-GCCcore-6.4.0, 1.11.3-intel-2016a, 1.11.10-GCCcore-7.3.0, 1.11.8

Command: module load hwloc

HMMER

Homepage: http://hmmer.org/

Description: HMMER is used for searching sequence databases for homologs of protein sequences,and for making protein sequence alignments. It implements methods using probabilistic modelscalled profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and othersequence alignment and database search tools based on older scoring methodology,HMMER aims to be significantly more accurate and more able to detect remote homologsbecause of the strength of its underlying mathematical models. In the past, this strengthcame at significant computational expense, but in the new HMMER3 project, HMMER is nowessentially as fast as BLAST.

Available versions: 3.1b2-intel-2016a

Command: module load HMMER

hdf5

Available versions: 1.10.1

Command: module load hdf5

hdf5_18

Available versions: 1.8.20

Command: module load hdf5_18

hpl

Available versions: 2.2

Command: module load hpl

intel

Available versions: compiler/64/ps_2016/2016.0.047

Command: module load rc/intel

IMPUTE2

Available versions: 2.3.0_x86_64_static, 2.3.2_x86_64_static

Command: module load IMPUTE2

IPython

Available versions: 3.2.0-intel-2015b-Python-2.7.9, 5.0.0-foss-2016a-Python-3.5.1

Command: module load IPython

icc

Homepage: http://software.intel.com/en-us/intel-compilers/

Description: C and C++ compiler from Intel

Available versions: 2015.3.187, 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load icc

iccifort

Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI andIntel MKL

Available versions: 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load iccifort

ifort

Homepage: http://software.intel.com/en-us/intel-compilers/

Description: Fortran compiler from Intel

Available versions: 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load ifort

iimpi

Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Description: Intel C/C++ and Fortran compilers, alongside Intel MPI.

Available versions: 7.3.5-GNU-4.9.3-2.25, 8.1.5-GCC-4.9.3-2.25, 2017a, 2016b

Command: module load iimpi

imkl

Homepage: http://software.intel.com/en-us/intel-mkl/

Description: Intel Math Kernel Library is a library of highly optimized,extensively threaded math routines for science, engineering, and financialapplications that require maximum performance. Core math functions includeBLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

Available versions: 11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25, 11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25, 2017.1.132-iimpi-2017a, 11.3.3.210-iimpi-2016b

Command: module load imkl

impi

Homepage: http://software.intel.com/en-us/intel-mpi-library/

Description: The Intel(R) MPI Library for Linux* OS is a multi-fabric messagepassing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library forLinux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.

Available versions: 5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25, 5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25, 2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27, 5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26

Command: module load impi

inputproto

Available versions: 2.3-foss-2016a, 2.3.1-foss-2015b, 2.3.1-foss-2016a, 2.3.1-foss-2016b, 2.3.1-goolf-1.7.20, 2.3.1-intel-2015b, 2.3.1-intel-2016a

Command: module load inputproto

intel

Available versions: 2015b, 2016a, 2017a, 2016b, mic/sdk/3.8.4

Command: module load intel

ITK

Homepage: https://itk.org

Description: Insight Segmentation and Registration Toolkit (ITK) providesan extensive suite of software tools for registering and segmentingmultidimensional imaging data.

Available versions: 4.12.2-foss-2016b-Python-2.7.12

Command: module load ITK

ICU

Homepage: http://site.icu-project.org/home

Description: ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalizationsupport for software applications.

Available versions: 61.1-GCCcore-6.4.0

Command: module load ICU

ipmitool

Available versions: 1.8.18

Command: module load ipmitool

intel-tbb-oss

Available versions: ia32/2018_20180618oss, intel64/2018_20180618oss

Command: module load intel-tbb-oss

iozone

Available versions: 3_471

Command: module load iozone

jspr

Available versions: 2017-7-20

Command: module load rc/jspr

JAGS

Available versions: 3.4.0-goolf-1.4.10

Command: module load JAGS

JUnit

Available versions: 4.12-Java-1.7.0_80, 4.12-Java-1.8.0_92

Command: module load JUnit

Java

Available versions: 1.7.0_10, 1.7.0_15, 1.7.0_21, 1.7.0_80, 1.8.0_112, 1.8.0_25, 1.8.0_45, 1.8.0_60, 1.8.0_72, 1.8.0_74, 1.8.0_92, 1.8.0_121, 1.8.0_144, 1.8.0_141, 1.8.0_152, 1.8.0_162, .modulerc

Command: module load Java

Jellyfish

Homepage: http://www.genome.umd.edu/jellyfish.html

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Available versions: 2.2.4-intel-2015b, 2.2.6-foss-2016b

Command: module load Jellyfish

jupyterhub

Available versions: 0.6.1-foss-2016a-Python-3.5.1

Command: module load jupyterhub

Kent_tools

Available versions: 340

Command: module load Kent_tools

Kerberos_V5

Available versions: 1.12.2-intel-2015b

Command: module load Kerberos_V5

kbproto

Available versions: 1.0.6-foss-2015b, 1.0.6-foss-2016a, 1.0.6-goolf-1.7.20, 1.0.6-intel-2016a, 1.0.7-foss-2016a, 1.0.7-foss-2016b, 1.0.7-goolf-1.7.20, 1.0.7-intel-2015b, 1.0.7-intel-2016a

Command: module load kbproto

KING

Homepage: http://people.virginia.edu/~wc9c/KING/

Description: KING is a toolset making use of high-throughput SNPdata typically seen in a genome-wide association study (GWAS) or asequencing project. Applications of KING include family relationshipinference and pedigree error checking, population substructureidentification, forensics, gene mapping, etc.

Available versions: 2.1.2-foss-2016a

Command: module load KING

kallisto

Homepage: http://pachterlab.github.io/kallisto/

Description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generallyof target sequences using high-throughput sequencing reads.

Available versions: 0.43.1-intel-2017a

Command: module load kallisto

lstc

Available versions: lsdyna

Command: module load rc/lstc

lumpy

Available versions: 0.2.13

Command: module load rc/lumpy

lcmodel

Available versions: 6.3

Command: module load rc/lcmodel

luajit

Available versions: 2.0.5

Command: module load rc/luajit

libarchive

Available versions: 3.1.2-10

Command: module load rc/libarchive

LAPACK

Available versions: 3.4.2-gompi-1.5.12

Command: module load LAPACK

LeadIT

Available versions: 2.1.9

Command: module load LeadIT

LibTIFF

Homepage: http://www.remotesensing.org/libtiff/

Description: tiff: Library and tools for reading and writing TIFF data files

Available versions: 4.0.3-foss-2016b, 4.0.4-goolf-1.7.20, 4.0.4-intel-2015b, 4.0.6-foss-2016b, 4.0.6-intel-2015b, 4.0.6-intel-2016a, 4.0.7-intel-2017a, 4.0.8-intel-2017a, 3.9.7-intel-2016a, 4.0.6-intel-2016b, 4.0.9-GCCcore-6.4.0, 4.0.7-foss-2016b, 4.0.9-GCCcore-5.4.0

Command: module load LibTIFF

Lmod

Available versions: 6.3-GCC-4.8.4

Command: module load Lmod

LocusZoom

Available versions: 1.3-goolf-1.7.20

Command: module load LocusZoom

Lua

Available versions: 5.1.4-8-GCC-4.8.4

Command: module load Lua

lftp

Available versions: 4.6.4-GNU-4.9.3-2.25

Command: module load lftp

libGLU

Homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/

Description: The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

Available versions: 9.0.0-foss-2016b, 9.0.0-intel-2016a, 9.0.0-intel-2016a-Mesa-11.2.1, 9.0.0-intel-2017a, 9.0.0-foss-2018a

Command: module load libGLU

libICE

Available versions: 1.0.8-foss-2016a, 1.0.8-intel-2016a, 1.0.9-foss-2016a, 1.0.9-foss-2016b, 1.0.9-intel-2015b, 1.0.9-intel-2016a

Command: module load libICE

libSM

Available versions: 1.2.1-foss-2016a, 1.2.1-intel-2016a, 1.2.2-foss-2016a, 1.2.2-foss-2016b, 1.2.2-intel-2015b, 1.2.2-intel-2016a

Command: module load libSM

libX11

Available versions: 1.6.1-foss-2016a, 1.6.3-foss-2016a, 1.6.3-foss-2016b, 1.6.3-goolf-1.7.20, 1.6.3-goolf-1.7.20-Python-2.7.9, 1.6.3-intel-2015b, 1.6.3-intel-2015b-Python-2.7.10, 1.6.3-intel-2016a

Command: module load libX11

libXau

Available versions: 1.0.8-foss-2015b, 1.0.8-foss-2016a, 1.0.8-foss-2016b, 1.0.8-goolf-1.7.20, 1.0.8-intel-2015b, 1.0.8-intel-2016a

Command: module load libXau

libXcursor

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X Cursor management library

Available versions: 1.1.14-intel-2016a, 1.1.14-foss-2016b

Command: module load libXcursor

libXdamage

Available versions: 1.1.4-foss-2016b, 1.1.4-goolf-1.7.20, 1.1.4-intel-2016a

Command: module load libXdamage

libXdmcp

Homepage: http://www.freedesktop.org/wiki/Software/xlibs}

Available versions: 1.1.1-intel-2016a, 1.1.2-foss-2015b, 1.1.2-foss-2016a, 1.1.2-foss-2016b, 1.1.2-goolf-1.7.20, 1.1.2-intel-2015b, 1.1.2-intel-2016a

Command: module load libXdmcp

libXext

Available versions: 1.3.3-foss-2016a, 1.3.3-foss-2016b, 1.3.3-goolf-1.7.20, 1.3.3-intel-2015b, 1.3.3-intel-2016a

Command: module load libXext

libXfixes

Available versions: 5.0.1-foss-2016b, 5.0.1-goolf-1.7.20, 5.0.1-intel-2015b, 5.0.1-intel-2016a

Command: module load libXfixes

libXfont

Available versions: 1.5.1-foss-2016b, 1.5.1-goolf-1.7.20, 1.5.1-intel-2016a, 1.5.1-intel-2016a-freetype-2.6.3

Command: module load libXfont

libXft

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X11 client-side library

Available versions: 2.3.2-foss-2016a, 2.3.2-intel-2016a, 2.3.2-foss-2016b

Command: module load libXft

libXi

Available versions: 1.7.4-intel-2015b, 1.7.6-goolf-1.7.20, 1.7.6-intel-2016a

Command: module load libXi

libXinerama

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: Xinerama multiple monitor library

Available versions: 1.1.3-intel-2016a, 1.1.3-foss-2016b

Command: module load libXinerama

libXmu

Available versions: 1.1.2-foss-2016a, 1.1.2-intel-2016a

Command: module load libXmu

libXp

Available versions: 1.0.3-foss-2016a, 1.0.3-goolf-1.7.20, 1.0.3-intel-2016a

Command: module load libXp

libXpm

Available versions: 3.5.11-foss-2016a, 3.5.11-intel-2016a

Command: module load libXpm

libXrandr

Available versions: 1.5.0-goolf-1.7.20, 1.5.0-intel-2016a

Command: module load libXrandr

libXrender

Available versions: 0.9.9-foss-2016a, 0.9.9-foss-2016b, 0.9.9-goolf-1.7.20, 0.9.9-intel-2015b, 0.9.9-intel-2016a

Command: module load libXrender

libXt

Available versions: 1.1.4-foss-2016a, 1.1.5-foss-2016a, 1.1.5-foss-2016b, 1.1.5-intel-2015b, 1.1.5-intel-2016a

Command: module load libXt

libcerf

Available versions: 1.4-foss-2016b, 1.4-intel-2016a

Command: module load libcerf

libdrm

Homepage: http://dri.freedesktop.org

Description: Direct Rendering Manager runtime library.

Available versions: 2.4.67-foss-2016b, 2.4.67-goolf-1.7.20, 2.4.67-intel-2016a, 2.4.68-intel-2016a, 2.4.70-foss-2016b, 2.4.76-intel-2017a, 2.4.88-GCCcore-6.4.0, 2.4.91-GCCcore-6.4.0, 2.4.91-GCCcore-5.4.0

Command: module load libdrm

libfontenc

Available versions: 1.1.3-foss-2016b, 1.1.3-goolf-1.7.20, 1.1.3-intel-2016a

Command: module load libfontenc

libgcrypt

Homepage: https://gnupg.org/related_software/libgcrypt/index.html

Description: Libgpg-error is a small library that defines common error values for all GnuPG components.

Available versions: 1.6.5-intel-2016a, 1.6.5-foss-2016a, 1.6.5-intel-2017a

Command: module load libgcrypt

libgd

Homepage: https://libgd.github.io/

Description: GD is an open source code library for the dynamic creation of images by programmers.

Available versions: 2.1.0-intel-2016a, 2.1.1-foss-2016b, 2.1.1-intel-2016a, 2.2.3-intel-2016a, 2.2.4-intel-2017a

Command: module load libgd

libglade

Available versions: 2.6.4-intel-2016a

Command: module load libglade

libgpg-error

Homepage: https://gnupg.org/related_software/libgpg-error/index.html

Description: Libgpg-error is a small library that defines common error values for all GnuPG components.

Available versions: 1.21-intel-2016a, 1.21-foss-2016a, 1.21-foss-2016b, 1.21-intel-2017a

Command: module load libgpg-error

libgtextutils

Available versions: 0.6.1-intel-2015b

Command: module load libgtextutils

libidn

Available versions: 1.32-GNU-4.9.3-2.25

Command: module load libidn

libjpeg-turbo

Homepage: http://sourceforge.net/projects/libjpeg-turbo/

Description: libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD toaccelerate baseline JPEG compression and decompression. libjpeg is a librarythat implements JPEG image encoding, decoding and transcoding.

Available versions: 1.3.1-intel-2016a, 1.4.0-goolf-1.7.20, 1.4.1-foss-2015b, 1.4.2-foss-2016a, 1.4.2-foss-2016b, 1.4.2-intel-2015b, 1.4.2-intel-2016a, 1.5.0-foss-2016a, 1.5.0-foss-2016b, 1.5.0-intel-2015b, 1.5.0-intel-2016a, 1.5.1-intel-2017a, 1.5.2-GCCcore-6.3.0, 1.5.2-GCCcore-6.4.0, 1.5.0-intel-2017a, 1.5.0-intel-2016b, 1.5.3-GCCcore-6.4.0, 1.5.1-foss-2016b, 1.5.3-GCCcore-5.4.0

Command: module load libjpeg-turbo

libpciaccess

Available versions: 0.13.4-foss-2016b, 0.13.4-goolf-1.7.20, 0.13.4-intel-2016a

Command: module load libpciaccess

libpthread-stubs

Available versions: 0.3-foss-2015b, 0.3-foss-2016a, 0.3-foss-2016b, 0.3-goolf-1.7.20, 0.3-intel-2015b, 0.3-intel-2016a

Command: module load libpthread-stubs

libsodium

Available versions: 1.0.8-foss-2016a

Command: module load libsodium

libtasn1

Available versions: 4.7-GNU-4.9.3-2.25

Command: module load libtasn1

libtool

Homepage: http://www.gnu.org/software/libtool

Description: GNU libtool is a generic library support script. Libtool hides the complexity of using shared librariesbehind a consistent, portable interface.

Available versions: 2.4.2-foss-2016a, 2.4.2-intel-2016a, 2.4.5-GCC-4.8.4, 2.4.6, 2.4.6-GCC-4.8.4, 2.4.6-GCC-4.9.3-2.25, 2.4.6-GNU-4.9.3-2.25, 2.4.6-foss-2016a, 2.4.6-foss-2016b, 2.4.6-goolf-1.7.20, 2.4.6-intel-2015b, 2.4.6-intel-2016a, 2.4.6-GCCcore-6.3.0, 2.4.6-GCC-5.4.0-2.26, 2.4.6-intel-2017a, 2.4.6-GCCcore-6.4.0, 2.4.6-GCCcore-7.3.0, 2.4.6-GCCcore-5.4.0

Command: module load libtool

libunistring

Available versions: 0.9.3-GNU-4.9.3-2.25

Command: module load libunistring

libxcb

Available versions: 1.11-goolf-1.7.20-Python-2.7.9, 1.11.1-foss-2016a, 1.11.1-foss-2016b, 1.11.1-goolf-1.7.20, 1.11.1-intel-2015b, 1.11.1-intel-2015b-Python-2.7.10, 1.11.1-intel-2016a, 1.8-foss-2016a-Python-2.7.3

Command: module load libxcb

libxkbcommon

Available versions: 0.6.1-intel-2016a

Command: module load libxkbcommon

libxslt

Homepage: http://xmlsoft.org/

Description: Libxslt is the XSLT C library developed for the GNOME project(but usable outside of the Gnome platform).

Available versions: 1.1.28-intel-2016a, 1.1.28-foss-2016a, 1.1.29-intel-2016a, 1.1.32-intel-2016a, 1.1.29-intel-2017a

Command: module load libxslt

libsndfile

Homepage: http://www.mega-nerd.com/libsndfile

Description: Libsndfile is a C library for reading and writing files containing sampled sound(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.

Available versions: 1.0.28-intel-2017a, 1.0.28-GCCcore-6.4.0

Command: module load libsndfile

libyaml

Homepage: http://pyyaml.org/wiki/LibYAML

Description: LibYAML is a YAML 1.1 parser and emitter written in C.

Available versions: 0.1.6-intel-2016a, 0.1.6-intel-2017a, 0.1.7-intel-2016a

Command: module load libyaml

libspatialindex

Homepage: http://libspatialindex.github.io

Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API

Available versions: 1.8.5-foss-2016b, 1.8.5-intel-2016a

Command: module load libspatialindex

libspatialite

Homepage: https://www.gaia-gis.it/fossil/libspatialite/home

Description: SpatiaLite is an open source library intended to extend the SQLite core to supportfully fledged Spatial SQL capabilities.

Available versions: 4.3.0a-foss-2016b, 4.3.0a-intel-2016a

Command: module load libspatialite

LoFreq

Homepage: http://csb5.github.io/lofreq

Description: Fast and sensitive variant calling from next-gen sequencing data

Available versions: 2.1.2-intel-2017a-Python-2.7.12

Command: module load LoFreq

LibUUID

Homepage: http://sourceforge.net/projects/libuuid/

Description: Portable uuid C library

Available versions: 1.0.3-foss-2016a

Command: module load LibUUID

LAME

Homepage: http://lame.sourceforge.net/

Description: LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

Available versions: 3.99.5-foss-2016b

Command: module load LAME

LZO

Homepage: http://www.oberhumer.com/opensource/lzo/

Description: Portable lossless data compression library

Available versions: 2.10-foss-2016b

Command: module load LZO

libgeotiff

Homepage: https://directory.fsf.org/wiki/Libgeotiff

Description: Library for reading and writing coordinate system information from/to GeoTIFF files

Available versions: 1.4.2-foss-2018a

Command: module load libgeotiff

lua

Available versions: 5.3.4

Command: module load lua

lapack

Available versions: gcc/64/3.8.0

Command: module load lapack

MEGA2

Available versions: 4.9.1

Command: module load rc/MEGA2

Mathematica

Available versions: 10.3

Command: module load rc/Mathematica

manta

Available versions: 1.0.3

Command: module load rc/manta

mat

Available versions: test

Command: module load rc/mat

matlab

Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b, R2019a

Command: module load rc/matlab

metasv

Available versions: 0.5.2

Command: module load rc/metasv

mriconvert

Available versions: 2.0.8

Command: module load rc/mriconvert

maskface

Available versions: 12272017

Command: module load rc/maskface

M4

Homepage: http://www.gnu.org/software/m4/m4.html

Description: GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatiblealthough it has some extensions (for example, handling more than 9 positional parameters to macros).GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

Available versions: 1.4.16-foss-2016a, 1.4.17, 1.4.17-GCC-4.8.4, 1.4.17-GCC-4.9.3-2.25, 1.4.17-GCC-4.9.3-binutils-2.25, 1.4.17-GCCcore-4.9.3, 1.4.17-GCCcore-5.4.0, 1.4.17-GNU-4.9.3-2.25, 1.4.17-foss-2016a, 1.4.17-foss-2016b, 1.4.17-goolf-1.7.20, 1.4.17-intel-2015b, 1.4.17-intel-2016a, 1.4.18-GCCcore-6.3.0, 1.4.17-GCCcore-6.1.0, 1.4.17-GCC-5.4.0-2.26, 1.4.17-intel-2017a, 1.4.16, 1.4.18, 1.4.18-GCCcore-6.4.0, 1.4.18-GCCcore-7.3.0, 1.4.18-GCCcore-5.4.0

Command: module load M4

MACH

Available versions: 1.0.18

Command: module load MACH

MACS

Available versions: 1.4.2-1-goolf-1.7.20-Python-2.7.5

Command: module load MACS

MOSAIK

Homepage: https://code.google.com/p/mosaik-aligner/

Description: MOSAIK is a reference-guided aligner for next-generationsequencing technologies

Available versions: 2.2.28-intel-2016a-20140425-24cf06

Command: module load MOSAIK

MPICH

Available versions: 3.0.4-GCC-4.8.1

Command: module load MPICH

MRIcroGL

Available versions: 09302016

Command: module load MRIcroGL

MRIcron

Available versions: 06_22_15

Command: module load MRIcron

MRtrix

Available versions: 0.3.14-intel-2016a-Python-2.7.11, 0.3.16-intel-2016a-Python-2.7.11

Command: module load MRtrix

MUSCLE

Homepage: http://drive5.com/muscle/

Description: MUSCLE is one of the best-performing multiple alignment programsaccording to published benchmark tests, with accuracy and speed that are consistentlybetter than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most userslearn everything they need to know about MUSCLE in a few minutes—only a handful ofcommand-line options are needed to perform common alignment tasks.

Available versions: 3.8.31-intel-2016a

Command: module load MUSCLE

MVAPICH2

Available versions: 2.2b-GCC-4.9.3-2.25

Command: module load MVAPICH2

Maq

Available versions: 0.7.0

Command: module load Maq

Mathematica

Available versions: 11.0.1

Command: module load Mathematica

Maven

Homepage: http://maven.apache.org/index.html}

Available versions: 3.3.9

Command: module load Maven

Mercurial

Homepage: http://mercurial.selenic.com/

Description: Mercurial is a free, distributed source control management tool. It efficiently handles projectsof any size and offers an easy and intuitive interface.

Available versions: 2.5.2-goolf-1.7.20-Python-2.7.3, 3.8.3-foss-2016a-Python-2.7.11, 3.8.3-intel-2016a-Python-2.7.11, 3.2.4-foss-2015b-Python-2.7.9

Command: module load Mercurial

Mesa

Homepage: http://www.mesa3d.org/

Description: Mesa is an open-source implementation of the OpenGL specification -a system for rendering interactive 3D graphics.

Available versions: 11.1.2-intel-2016a, 11.2.1-intel-2016a, 12.0.2-foss-2016b, 17.0.2-intel-2017a, 17.3.6-foss-2018a, 11.1.2-foss-2016b

Command: module load Mesa

Minimac2

Available versions: 2014.9.15-intel-2015b

Command: module load Minimac2

Minimac3

Available versions: 1.0.10-intel-2015b

Command: module load Minimac3

makedepend

Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html

Description: The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.

Available versions: 1.0.5-intel-2016a, 1.0.5-foss-2016b

Command: module load makedepend

matplotlib

Homepage: http://matplotlib.org

Description: matplotlib is a python 2D plotting library which produces publication quality figures in a variety ofhardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the pythonand ipython shell, web application servers, and six graphical user interface toolkits.

Available versions: 1.3.1-intel-2015b-Python-2.7.8, 1.5.1-intel-2016a-Python-2.7.11, 1.5.3-foss-2016b-Python-2.7.12, 2.0.0-foss-2016b-Python-2.7.12, 2.0.2-foss-2016b-Python-2.7.12, 2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29, 1.5.1-foss-2016a-Python-2.7.11

Command: module load matplotlib

motif

Available versions: 2.3.5-foss-2016a, 2.3.5-intel-2016a, 2.3.7-intel-2016a

Command: module load motif

MACS2

Homepage: https://github.com/taoliu/MACS/

Description: Model Based Analysis for ChIP-Seq data

Available versions: 2.1.0.20150731-foss-2016a-Python-2.7.11, 2.1.1.20160309-foss-2016a-Python-2.7.11

Command: module load MACS2

MEME

Homepage: http://meme-suite.org/

Description: The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) orGLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs usingMAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associatemotifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichmentusing SpaMo or CentriMo.

Available versions: 4.12.0-foss-2016a

Command: module load MEME

MultiQC

Available versions: 0.9-foss-2016b-Python-2.7.12, 1.2-foss-2016b-Python-2.7.12, 1.4-foss-2016b-Python-2.7.12, 0.8, 0.8~

Command: module load MultiQC

Mono

Homepage: http://www.mono-project.com/

Description: An open source, cross-platform, implementation of C# and the CLR that isbinary compatible with Microsoft.NET.

Available versions: 4.8.0.495-intel-2017a, 5.2.0.224-intel-2017a

Command: module load Mono

MaSuRCA

Homepage: http://www.genome.umd.edu/masurca.html

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graphand Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containingonly short reads from Illumina sequencing or a mixture of short reads and long reads(Sanger, 454, Pacbio and Nanopore).

Available versions: 3.2.4-foss-2018a, 3.2.6-foss-2018a

Command: module load MaSuRCA

minimap2

Homepage: https://github.com/lh3/minimap2

Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps betweenlong noisy reads, or map long reads or their assemblies to a reference genome optionally with detailedalignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limitedtest data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replaceBWA-MEM for long reads and contig alignment.

Available versions: 2.0rc1-foss-2016b

Command: module load minimap2

MotionCor2

Homepage: http://msg.ucsf.edu/em/software/motioncor2.html

Description: MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recordedon dose fractionated movie stacks

Available versions: 1.0.4, 1.0.5

Command: module load MotionCor2

mpich

Available versions: ge/gcc/64/3.2.1

Command: module load mpich

mpiexec

Available versions: 0.84_432

Command: module load mpiexec

mvapich2

Available versions: gcc/64/2.3b

Command: module load mvapich2

NAMD

Available versions: 2.12b1-gpu, 2.12, 2.13b2-gpu

Command: module load rc/NAMD

nccl

Homepage: https://developer.nvidia.com/nccl

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs.

Available versions: 1.3.4-1

Command: module load rc/nccl

ncdu

Available versions: 1.13-20.1

Command: module load rc/ncdu

nighres

Available versions: 1.1.0b1

Command: module load rc/nighres

NASM

Homepage: http://www.nasm.us/

Description: NASM: General-purpose x86 assembler

Available versions: 2.07-intel-2015b, 2.07-intel-2016a, 2.11.06-goolf-1.7.20, 2.11.08-foss-2015b, 2.11.08-foss-2016a, 2.11.08-foss-2016b, 2.11.08-intel-2015b, 2.11.08-intel-2016a, 2.12.02-foss-2016a, 2.12.02-foss-2016b, 2.12.02-intel-2015b, 2.12.02-intel-2016a, 2.12.02-intel-2017a, 2.13.01-GCCcore-6.3.0, 2.13.01-GCCcore-6.4.0, 2.12.02-intel-2016b, 2.13.03-GCCcore-6.4.0, 2.13.03-GCCcore-5.4.0

Command: module load NASM

NGS

Available versions: 1.2.5-foss-2016b

Command: module load NGS

ncbi-vdb

Available versions: 2.7.0-foss-2016b

Command: module load ncbi-vdb

netCDF

Homepage: http://www.unidata.ucar.edu/software/netcdf/

Description: NetCDF (network Common Data Form) is a set of software librariesand machine-independent data formats that support the creation, access, and sharing of array-orientedscientific data.

Available versions: 4.3.3.1-foss-2016a, 4.3.3.1-intel-2016a, 4.4.0-intel-2016a, 4.4.1-foss-2016a, 4.4.1-foss-2016b, 4.4.1-intel-2015b, 4.4.1-intel-2016a, 4.4.1.1-intel-2017a, 4.4.1.1-foss-2016b, 4.4.1.1-intel-2016a, 4.6.0-foss-2018a

Command: module load netCDF

nodejs

Available versions: 4.4.7-foss-2016a

Command: module load nodejs

numactl

Homepage: http://oss.sgi.com/projects/libnuma/

Description: The numactl program allows you to run your application program on specificcpu's and memory nodes. It does this by supplying a NUMA memory policy tothe operating system before running your program. The libnuma library providesconvenient ways for you to add NUMA memory policies into your own program.

Available versions: 2.0.10-GCC-4.8.4, 2.0.10-GNU-4.9.3-2.25, 2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25, 2.0.11-GCC-4.9.3-2.25, 2.0.11-GCC-5.4.0-2.26, 2.0.11-GCCcore-6.3.0, 2.0.11-intel-2017a, 2.0.11-GCC-6.1.0-2.27, 2.0.11-GCC-6.3.0-2.27, 2.0.11-GCCcore-6.4.0, 2.0.11-intel-2016a, 2.0.11-GCCcore-7.3.0

Command: module load numactl

numpy

Homepage: http://www.numpy.org

Description: NumPy is the fundamental package for scientific computing with Python. It contains among other things:a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortrancode, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses,NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can bedefined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

Available versions: 1.10.4-intel-2016a-Python-2.7.11, 1.8.2-intel-2015b-Python-2.7.11, 1.8.2-foss-2016a-Python-2.7.11, 1.10.1-goolf-1.7.20-Python-2.7.11

Command: module load numpy

NLopt

Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt

Description: NLopt is a free/open-source library for nonlinear optimization,providing a common interface for a number of different free optimization routinesavailable online as well as original implementations of various other algorithms.

Available versions: 2.4.2-intel-2017a, 2.4.2-foss-2016b, 2.4.2-foss-2018a

Command: module load NLopt

NiBabel

Homepage: https://nipy.github.io/nibabel

Description: NiBabel provides read/write access to some common medical and neuroimaging file formats,including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECATas well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry andannotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

Available versions: 2.1.0-intel-2017a-Python-2.7.13

Command: module load NiBabel

ngmlr

Homepage: https://github.com/philres/ngmlr

Description: Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to areference genome with a focus on reads that span structural variations.

Available versions: 0.2.6-foss-2016b

Command: module load ngmlr

NCBI-Toolkit

Homepage: http://ncbi.github.io/cxx-toolkit/

Description: The NCBI Toolkit is a collection of utilities developed for theproduction and distribution of GenBank, Entrez, BLAST, and related servicesby the National Center for Biotechnology Information.

Available versions: 18.0.0-intel-2017a

Command: module load NCBI-Toolkit

NCCL

Homepage: https://developer.nvidia.com/nccl

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs.

Available versions: 2.2.13-CUDA-9.2.148.1, 2.2.13-CUDA-8.0.61

Command: module load NCCL

netcdf

Available versions: gcc/64/4.5.0

Command: module load netcdf

netperf

Available versions: 2.7.0

Command: module load netperf

openscenegraph

Available versions: 3.2.1

Command: module load rc/openscenegraph

OTF

Available versions: 1.12.4-gompi-1.5.12

Command: module load OTF

OpenPGM

Available versions: 5.2.122-foss-2016a, 5.2.122-intel-2015b

Command: module load OpenPGM

OpenSSL

Homepage: http://www.openssl.org/

Description: The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured,and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1)protocols as well as a full-strength general purpose cryptography library.

Available versions: 1.0.2g-GCCcore-4.9.3, 1.0.2h-foss-2016b

Command: module load OpenSSL

OpenMM

Homepage: https://simtk.org/home/openmm

Description: OpenMM is a toolkit for molecular simulation.

Available versions: 6.3-intel-2016a-Python-2.7.11

Command: module load OpenMM

openmpi

Available versions: mlnx/gcc/64/3.1.1rc1, gcc/64/1.10.7

Command: module load openmpi

openblas

Available versions: .version, dynamic/0.2.20

Command: module load openblas

parsync

Available versions: 1.69

Command: module load rc/parsync

PCRE

Homepage: http://www.pcre.org/

Description: The PCRE library is a set of functions that implement regular expressionpattern matching using the same syntax and semantics as Perl 5.

Available versions: 8.38-foss-2016a, 8.38-foss-2016b, 8.38-intel-2015b, 8.38-intel-2016a, 8.39-intel-2015b, 8.39-intel-2016a, 8.39-foss-2016b, 8.40-intel-2017a, 8.41-GCCcore-6.3.0, 8.12-goolf-1.4.10, 8.12-intel-2016a, 8.41-GCCcore-6.4.0, 8.39-intel-2016b, 8.40-foss-2016b, 8.41-GCCcore-5.4.0

Command: module load PCRE

PDT

Available versions: 3.20-goolf-1.7.20

Command: module load PDT

PETSc

Available versions: 3.6.3-intel-2015b-Python-2.7.11

Command: module load PETSc

PGI

Homepage: http://www.pgroup.com/

Description: C, C++ and Fortran compilers from The Portland Group - PGI

Available versions: 17.10-GCC-6.3.0-2.27, 17.4-GCC-6.3.0-2.27, 18.5-GCC-6.4.0-2.28

Command: module load PGI

PHASE

Available versions: 2.1.1

Command: module load PHASE

PIL

Available versions: 1.1.7-intel-2015b-Python-2.7.11, 1.1.7-intel-2016a-Python-2.7.11

Command: module load PIL

PROJ

Homepage: http://trac.osgeo.org/proj/

Description: Program proj is a standard Unix filter function which convertsgeographic longitude and latitude coordinates into cartesian coordinates

Available versions: 4.9.2-foss-2016a, 4.9.2-foss-2016b, 4.9.2-intel-2015b, 4.9.2-intel-2016a, 4.9.3-intel-2017a, 4.9.3-foss-2016b, 4.9.3-intel-2016a, 5.0.0-foss-2018a

Command: module load PROJ

Pango

Homepage: http://www.pango.org/

Description: Pango is a library for laying out and rendering of text, with an emphasis on internationalization.Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

Available versions: 1.39.0-foss-2016b, 1.39.0-intel-2016a, 1.40.1-intel-2016a, 1.40.12-intel-2017a

Command: module load Pango

Pindel

Homepage: http://gmt.genome.wustl.edu/packages/pindel/

Description: Pindel can detect breakpoints of large deletions, medium sizedinsertions, inversions, tandem duplications and other structural variants at single-basedresolution from next-gen sequence data. It uses a pattern growth approach to identify thebreakpoints of these variants from paired-end short reads.

Available versions: 0.2.5b8-foss-2016b

Command: module load Pindel

ProbABEL

Available versions: 0.5.0

Command: module load ProbABEL

PyCairo

Available versions: 1.10.0-intel-2016a-Python-2.7.11

Command: module load PyCairo

PyGObject

Available versions: 2.28.6-intel-2016a-Python-2.7.11

Command: module load PyGObject

PyGTK

Available versions: 2.24.0-intel-2016a-Python-2.7.11

Command: module load PyGTK

PyQt

Available versions: 4.11.3-goolf-1.7.20-Python-2.7.9, 4.11.4-foss-2016a-Python-2.7.11, 4.11.4-intel-2016a-Python-2.7.11

Command: module load PyQt

PyZMQ

Available versions: 14.7.0-intel-2015b-Python-2.7.9-zmq3, 15.3.0-foss-2016a-Python-3.5.1-zmq4

Command: module load PyZMQ

Pygments

Available versions: 2.0.2-intel-2015b-Python-2.7.9

Command: module load Pygments

Pysam

Available versions: 0.9.1.4-foss-2016a-Python-2.7.12, 0.9.1.4-foss-2016b-Python-2.7.12

Command: module load Pysam

p11-kit

Available versions: 0.23.2-GNU-4.9.3-2.25

Command: module load p11-kit

parallel

Available versions: 20150822-GCC-4.9.2

Command: module load parallel

path.py

Available versions: 8.2.1-foss-2016a-Python-3.5.1

Command: module load path.py

perl-app-cpanminus

Available versions: 1.7039

Command: module load perl-app-cpanminus

pixman

Homepage: http://www.pixman.org/

Description: Pixman is a low-level software library for pixel manipulation, providingfeatures such as image compositing and trapezoid rasterization. Importantusers of pixman are the cairo graphics library and the X server.

Available versions: 0.34.0-foss-2016b, 0.34.0-intel-2015b, 0.34.0-intel-2016a, 0.34.0-GCCcore-6.3.0, 0.34.0-GCCcore-6.4.0, 0.34.0-foss-2016a, 0.34.0-intel-2016b, 0.32.6-intel-2016a, 0.34.0-GCCcore-5.4.0

Command: module load pixman

pkgconfig

Available versions: 1.1.0-intel-2016a-Python-2.7.11

Command: module load pkgconfig

printproto

Available versions: 1.0.5-foss-2015b, 1.0.5-foss-2016a, 1.0.5-goolf-1.7.20, 1.0.5-intel-2016a

Command: module load printproto

prompt-toolkit

Available versions: 1.0.3-foss-2016a-Python-3.5.1

Command: module load prompt-toolkit

pysqlite

Available versions: 2.6.3-intel-2015b-Python-2.7.9

Command: module load pysqlite

protobuf

Homepage: https://github.com/google/protobuf/

Description: Google Protocol Buffers

Available versions: 3.3.0-intel-2017a

Command: module load protobuf

protobuf-python

Homepage: https://github.com/google/protobuf/

Description: Python Protocol Buffers runtime library.

Available versions: 3.3.0-intel-2017a-Python-3.6.1

Command: module load protobuf-python

PyYAML

Homepage: https://pypi.python.org/pypi/PyYAML/

Description: PyYAML is a YAML parser and emitter for the Python programming language.

Available versions: 3.12-intel-2016a-Python-3.5.1

Command: module load PyYAML

prodigal

Homepage: http://prodigal.ornl.gov/

Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)is a microbial (bacterial and archaeal) gene finding program developedat Oak Ridge National Laboratory and the University of Tennessee.

Available versions: 2.6.2-GCC-4.9.3-binutils-2.25

Command: module load prodigal

Pillow

Homepage: http://pillow.readthedocs.org/

Description: Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

Available versions: 4.3.0-intel-2017a-Python-2.7.13

Command: module load Pillow

p7zip

Homepage: http://p7zip.sourceforge.net/

Description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix.7-Zip is a file archiver with highest compression ratio.

Available versions: 9.38.1

Command: module load p7zip

patchelf

Homepage: http://nixos.org/patchelf.html

Description: PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

Available versions: 0.9-intel-2016a, 0.9-foss-2016b

Command: module load patchelf

PCRE2

Homepage: http://www.pcre.org/

Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntaxand semantics as Perl 5.

Available versions: 10.21-foss-2016b, 10.31-foss-2018a

Command: module load PCRE2

qdirstat

Available versions: 1.4

Command: module load rc/qdirstat

Qt

Available versions: 4.8.6-goolf-1.7.20, 4.8.7-foss-2016a, 4.8.7-foss-2016b, 4.8.7-intel-2016a

Command: module load Qt

Qwt

Homepage: http://qwt.sourceforge.net/

Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programswith a technical background.

Available versions: 6.1.3-foss-2016b, 6.1.3-intel-2016a

Command: module load Qwt

QwtPolar

Homepage: http://qwtpolar.sourceforge.net/

Description: The QwtPolar library contains classes for displaying values on a polar coordinate system.

Available versions: 1.1.1-foss-2016b, 1.1.1-intel-2016a

Command: module load QwtPolar

QUAST

Homepage: http://quast.sourceforge.net/quast

Description: QUAST evaluates genome assemblies.

Available versions: 4.4-foss-2016a-Python-2.7.11, 4.6.3-foss-2016a-Python-2.7.11

Command: module load QUAST

QIIME

Available versions: qiime-dependencies

Command: module load QIIME

QWRAP

Available versions: v3

Command: module load QWRAP

RStudio

Available versions: 1.0.136, 1.0.44

Command: module load rc/RStudio

relion

Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computerprogram that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D classaverages in electron cryo-microscopy (cryo-EM).

Available versions: 1.4, 2.0_beta, 2.1

Command: module load rc/relion

rserver

Available versions: 3.4.3, 3.5.2, 3.5.2_X11

Command: module load rc/rserver

R

Available versions: 2.15.3-goolf-1.7.20, 3.0.1-goolf-1.4.10-bare, 3.2.0-goolf-1.7.20, 3.2.1-goolf-1.7.20, 3.2.3-foss-2016a-bare, 3.2.3-intel-2016a-bare, 3.3.1-foss-2016b, 3.3.1-foss-2016b-no-X, 3.3.1-intel-2016a-bare, 3.4.1-intel-2017a-X11-20170314, 3.3.3-intel-2017a-X11-20170314, 3.4.3-intel-2017a-X11-20170314, .3.4.3-foss-2016b-X11-20160819.bak_20180502163551, 3.4.3-foss-2016b-X11-20160819, 3.5.0-intel-2017a-X11-20170314-bare, 3.5.0-foss-2018a-X11-20180131-bare, 3.5.1-foss-2018a-X11-20180131-bare, DESeq2.R-3.3.1-foss-2016b-no-X, DESeq2.R-3.4.3-intel-2017a-X11-20170314

Command: module load R

RAxML

Available versions: 8.1.1-goolf-1.4.10-mt-avx

Command: module load RAxML

RSeQC

Available versions: 2.6.3-goolf-1.7.20-Python-2.7.10-R-3.2.1

Command: module load RSeQC

Ruby

Available versions: 2.3.3

Command: module load Ruby

randrproto

Available versions: 1.5.0-goolf-1.7.20, 1.5.0-intel-2015b, 1.5.0-intel-2016a

Command: module load randrproto

renderproto

Available versions: 0.11-foss-2016a, 0.11-foss-2016b, 0.11-goolf-1.7.20, 0.11-intel-2015b, 0.11-intel-2016a

Command: module load renderproto

requests

Available versions: 2.7.0-intel-2015b-Python-2.7.9

Command: module load requests

ResMap

Homepage: http://resmap.sourceforge.net/

Description: ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI.It is an easy to use software package for computing the local resolution of 3D density mapsstudied in structural biology, primarily electron cryo-microscopy (cryo-EM).

Available versions: 1.1.4

Command: module load ResMap

RELION

Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computerprogram that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D classaverages in electron cryo-microscopy (cryo-EM).

Available versions: 2.1-intel-2016a-CUDA-8.0.44

Command: module load RELION

Rust

Homepage: https://www.rust-lang.org

Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults,and guarantees thread safety.

Available versions: 1.30.1-foss-2016b

Command: module load Rust

snakemakeslurm_local

Available versions: 4.8.0-1

Command: module load snakemakeslurm_local

SAS

Available versions: v9.4

Command: module load rc/SAS

Salmon

Available versions: 0.7.2

Command: module load rc/Salmon

soapsv

Available versions: 1.3

Command: module load rc/soapsv

snakemake

Available versions: 4.0.0, 4.8.0

Command: module load rc/snakemake

sublime_text

Available versions: 3

Command: module load rc/sublime_text

S.A.G.E.

Available versions: 6.3

Command: module load S.A.G.E.

SCOTCH

Available versions: 6.0.4-intel-2015b

Command: module load SCOTCH

SHRiMP

Available versions: 2.2.3-goolf-1.4.10

Command: module load SHRiMP

SIP

Available versions: 4.16.4-goolf-1.7.20-Python-2.7.9, 4.16.4-intel-2015b-Python-2.7.9, 4.16.8-intel-2015b-Python-2.7.9, 4.18-foss-2016a-Python-2.7.11, 4.18-intel-2016a-Python-2.7.11

Command: module load SIP

SOLAR-Eclipse

Available versions: 8.1.1

Command: module load SOLAR-Eclipse

SPAdes

Homepage: http://cab.spbu.ru/software/spades/

Description: Genome assembler for single-cell and isolates data sets

Available versions: 3.9.0-foss-2016a, 3.12.0-foss-2016b

Command: module load SPAdes

SPPARKS

Available versions: 07192016-intel-2016a

Command: module load SPPARKS

STAR-Fusion

Available versions: 0.8.0-goolf-1.4.10-Perl-5.16.3

Command: module load STAR-Fusion

STAR

Available versions: 2.5.1b-goolf-1.4.10, 2.5.2a-foss-2016a, 2.5.4b-intel-2017a, 2.5.4b-foss-2016b, 2.5.2b, 2.5.2b~

Command: module load STAR

SWIG

Homepage: http://www.swig.org/

Description: SWIG is a software development tool that connects programs written in C and C++ witha variety of high-level programming languages.

Available versions: 3.0.10-intel-2016a-Python-2.7.12-PCRE-8.39, 3.0.12-intel-2017a-Python-2.7.13, 3.0.11-foss-2016b-Python-2.7.12, 3.0.11-intel-2016a-Python-2.7.12, 3.0.8-intel-2016a-Python-2.7.11, 3.0.12-foss-2018a-Python-3.6.4, 3.0.12-foss-2018a-Python-2.7.14

Command: module load SWIG

ScientificPython

Available versions: 2.9.4-intel-2015b-Python-2.7.11

Command: module load ScientificPython

Spack

Available versions: 0.10.0

Command: module load Spack

scipy

Available versions: 0.17.0-intel-2016a-Python-2.7.11

Command: module load scipy

shapeit

Available versions: 2.r837.GLIBCv2.12_linux_x86_64

Command: module load shapeit

sympy

Available versions: 0.7.6.1-intel-2015b-Python-2.7.11

Command: module load sympy

SRA-Toolkit

Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std

Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing filesfrom the SRA database and writing (loading) files into the .sra format

Available versions: 2.5.4-1-centos_linux64, 2.8.2-1-centos_linux64

Command: module load SRA-Toolkit

sparsehash

Homepage: https://code.google.com/p/sparsehash/

Description: An extremely memory-efficient hash_mapimplementation. 2 bits/entry overhead! The SparseHash librarycontains several hash-map implementations, includingimplementations that optimize for space or speed.

Available versions: 2.0.2-foss-2016a

Command: module load sparsehash

Spark

Homepage: http://spark.apache.org

Description: Spark is Hadoop MapReduce done in memory

Available versions: 2.2.0-Hadoop-2.6-Java-1.8.0_144

Command: module load Spark

summovie

Homepage: http://grigoriefflab.janelia.org/unblur

Description: Movie frame sums can be calculated using summovie,which uses the alignment results from a prior run of Unblur.

Available versions: 1.0.2

Command: module load summovie

snakemakeslurm

Available versions: 4.8.0, 4.8.0-2, 4.8.0-1

Command: module load snakemakeslurm

scalapack

Available versions: openmpi/gcc/64/2.0.2

Command: module load scalapack

sge

Available versions: 2011.11p1

Command: module load sge

slurm

Available versions: 17.11.8

Command: module load slurm

tortoise

Available versions: 2.5.2b, 3.0.0, 3.1.2

Command: module load rc/tortoise

transdecoder

Available versions: 5.3.0

Command: module load rc/transdecoder

torch

Available versions: 7

Command: module load rc/torch

tarquin

Available versions: 4.3.10

Command: module load rc/tarquin

tcllib

Available versions: 1.19

Command: module load rc/tcllib

Tar

Available versions: 1.29-goolf-1.4.10

Command: module load Tar

Tk

Homepage: http://www.tcl.tk/

Description: Tk is an open source, cross-platform widget toolchain that provides a library of basic elements forbuilding a graphical user interface (GUI) in many different programming languages.

Available versions: 8.6.3-foss-2015b-no-X11, 8.6.3-goolf-1.7.20-no-X11, 8.6.3-intel-2015b-no-X11, 8.6.4-foss-2015b-no-X11, 8.6.4-foss-2016a-no-X11, 8.6.4-foss-2016b-no-X11, 8.6.4-goolf-1.7.20, 8.6.4-goolf-1.7.20-no-X11, 8.6.4-intel-2015b-no-X11, 8.6.4-intel-2016a-no-X11, 8.6.5-foss-2016a, 8.6.5-foss-2016b, 8.6.5-intel-2015b, 8.6.5-intel-2016a, 8.6.6-intel-2017a, 8.6.5-intel-2017a, 8.6.8-foss-2018a

Command: module load Tk

TopHat

Available versions: 2.1.0-intel-2015b, 2.1.1-foss-2016a

Command: module load TopHat

Trim_Galore

Available versions: 0.4.2-foss-2016b, 0.4.4-foss-2016b

Command: module load Trim_Galore

Trimmomatic

Available versions: 0.36-Java-1.8.0_92

Command: module load Trimmomatic

Trinity

Available versions: 2.2.0-foss-2016a

Command: module load Trinity

tabix

Available versions: 0.2.6-goolf-1.7.20, 0.2.6-intel-2015b

Command: module load tabix

tcsh

Available versions: 6.18.01-goolf-1.7.20, 6.18.01-intel-2015b, 6.19.00-foss-2015b, 6.19.00-foss-2016a, 6.19.00-foss-2016b, 6.19.00-intel-2016a

Command: module load tcsh

testpath

Available versions: 0.3-foss-2016a-Python-3.5.1

Command: module load testpath

texinfo

Homepage: https://www.gnu.org/software/texinfo/

Description: Texinfo is the official documentation format of the GNU project.

Available versions: 4.13a, 6.4-GCCcore-5.4.0

Command: module load texinfo

Tensorflow

Homepage: https://www.tensorflow.org/

Description: An open-source software library for Machine Intelligence

Available versions: 1.2.0-intel-2017a-Python-3.6.1

Command: module load Tensorflow

TransDecoder

Homepage: https://github.com/TransDecoder/TransDecoder/wiki

Description: TransDecoder identifies candidate coding regions within transcript sequences,such as those generated by de novo RNA-Seq transcript assembly using Trinity,or constructed based on RNA-Seq alignments to the genome usingTophat and Cufflinks.

Available versions: 5.1.0-intel-2017a-Perl-5.24.1

Command: module load TransDecoder

trim_galore

Available versions: 0.4.2, 0.4.2~

Command: module load trim_galore

torque

Available versions: 6.1.1

Command: module load torque

unblur

Homepage: http://grigoriefflab.janelia.org/unblur

Description: Unblur is used to align the frames of movies recorded on an electron microscopeto reduce image blurring due to beam-induced motion.It reads stacks of movies that are stored in MRC/CCP4 format.

Available versions: 1.0.2

Command: module load unblur

usearch

Available versions: 7.0.1090

Command: module load usearch

vmd

Available versions: 1.9.3

Command: module load rc/vmd

VEGAS

Available versions: 0.8.27

Command: module load VEGAS

VICUNA

Available versions: 1.3

Command: module load VICUNA

VPhaser-2

Available versions: 02112013-intel-2016a

Command: module load VPhaser-2

VTK

Homepage: http://www.vtk.org

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for3D computer graphics, image processing and visualization. VTK consists of a C++ class library and severalinterpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualizationalgorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniquessuch as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

Available versions: 7.1.1-intel-2017a-Python-2.7.13, 6.3.0-foss-2016b-Python-2.7.12

Command: module load VTK

VCFtools

Homepage: https://vcftools.github.io

Description: The aim of VCFtools is to provideeasily accessible methods for working with complexgenetic variation data in the form of VCF files.

Available versions: 0.1.14-intel-2016a-Perl-5.22.1, 0.1.15-intel-2016a-Perl-5.22.1

Command: module load VCFtools

wcwidth

Available versions: 0.1.7-foss-2016a-Python-3.5.1

Command: module load wcwidth

wxPython

Homepage: http://www.wxpython.org

Description: wxPython is a GUI toolkit for the Python programming language.It allows Python programmers to create programs with a robust,highly functional graphical user interface, simply and easily.It is implemented as a Python extension module (native code)that wraps the popular wxWidgets cross platform GUI library,which is written in C++.

Available versions: 3.0.2.0-intel-2017a-Python-2.7.13

Command: module load wxPython

wxWidgets

Homepage: http://www.wxwidgets.org/

Description: wxWidgets is a C++ library that lets developers create applications for Windows,Mac OS X, Linux and other platforms with a single code base.It has language bindings for Python, Perl, Ruby and many other languages.

Available versions: 3.0.3-intel-2016a, 3.0.3-foss-2016b

Command: module load wxWidgets

xget

Available versions: xget-public

Command: module load rc/xget

XKeyboardConfig

Available versions: 2.17-intel-2016a

Command: module load XKeyboardConfig

xbitmaps

Available versions: 1.1.1-foss-2016a, 1.1.1-intel-2016a

Command: module load xbitmaps

xcb-proto

Available versions: 1.11, 1.11-goolf-1.7.20-Python-2.7.9, 1.11-intel-2015b-Python-2.7.10, 1.7-foss-2016a-Python-2.7.3

Command: module load xcb-proto

xcb-util-image

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util-image

xcb-util-keysyms

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util-keysyms

xcb-util-renderutil

Available versions: 0.3.9-intel-2015b, 0.3.9-intel-2016a

Command: module load xcb-util-renderutil

xcb-util-wm

Available versions: 0.4.1-intel-2015b, 0.4.1-intel-2016a

Command: module load xcb-util-wm

xcb-util

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util

xextproto

Available versions: 7.2.1-foss-2016a, 7.2.1-intel-2016a, 7.3.0-foss-2015b, 7.3.0-foss-2016a, 7.3.0-foss-2016b, 7.3.0-goolf-1.7.20, 7.3.0-intel-2015b, 7.3.0-intel-2016a

Command: module load xextproto

xf86vidmodeproto

Available versions: 2.3.1-intel-2016a

Command: module load xf86vidmodeproto

xineramaproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X protocol and ancillary headers for xinerama

Available versions: 1.2.1-intel-2016a, 1.2.1-foss-2016b

Command: module load xineramaproto

xorg-macros

Available versions: 1.19.0-foss-2016a, 1.19.0-foss-2016b, 1.19.0-goolf-1.7.20, 1.19.0-intel-2016a

Command: module load xorg-macros

xprop

Homepage: http://www.x.org/wiki/

Description: The xprop utility is for displaying window and font properties in an X server.One window or font is selected using the command line arguments or possiblyin the case of a window, by clicking on the desired window. A list ofproperties is then given, possibly with formatting information.

Available versions: 1.2.2-intel-2016a, 1.2.2-intel-2017a, 1.2.2-foss-2016b

Command: module load xprop

xproto

Available versions: 7.0.23-foss-2016a, 7.0.26-intel-2016a, 7.0.27-foss-2015b, 7.0.27-goolf-1.7.20, 7.0.28-foss-2016a, 7.0.28-foss-2016b, 7.0.28-goolf-1.7.20, 7.0.28-intel-2015b, 7.0.28-intel-2016a

Command: module load xproto

xtrans

Homepage: http://www.freedesktop.org/wiki/Software/xlibs}

Available versions: 1.2-foss-2016a, 1.3.4-intel-2016a, 1.3.5-foss-2015b, 1.3.5-foss-2016a, 1.3.5-foss-2016b, 1.3.5-goolf-1.7.20, 1.3.5-intel-2015b, 1.3.5-intel-2016a

Command: module load xtrans

Xerces-C++

Homepage: http://xerces.apache.org/xerces-c/

Description: Xerces-C++ is a validating XML parser written in a portablesubset of C++. Xerces-C++ makes it easy to give your application the ability toread and write XML data. A shared library is provided for parsing, generating,manipulating, and validating XML documents using the DOM, SAX, and SAX2APIs.

Available versions: 3.1.2-intel-2015b

Command: module load Xerces-C++

XQilla

Homepage: http://xqilla.sourceforge.net/HomePage

Description: XQilla is an XQuery and XPath 2 library and command line utility written in C++,implemented on top of the Xerces-C++ library.

Available versions: 2.3.2-intel-2015b

Command: module load XQilla

x264

Homepage: http://www.videolan.org/developers/x264.html

Description: x264 is a free software library and application for encoding video streams into the H.264/MPEG-4AVC compression format, and is released under the terms of the GNU GPL.

Available versions: 20160614-foss-2016b

Command: module load x264

x265

Homepage: http://x265.org/

Description: x265 is a free software library and application for encoding video streams into the H.265AVC compression format, and is released under the terms of the GNU GPL.

Available versions: 2.4-foss-2016b

Command: module load x265

Yasm

Homepage: http://www.tortall.net/projects/yasm/

Description: Yasm: Complete rewrite of the NASM assembler with BSD license

Available versions: 1.3.0-intel-2015b, 1.3.0-foss-2016b

Command: module load Yasm

zlib

Homepage: http://www.zlib.net/

Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.

Available versions: 1.2.10, 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a

Command: module load zlib

ZeroMQ

Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a

Command: module load ZeroMQ


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