NgsCctsBuildVicuna

Build/Install Broad's Vicuna

pre-requisites

NCBI toolkit 7.0.0

NOTE: This takes a veyr long time!!!

 # download
 cd /share/apps/ngs-ccts/downloads
 wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/7_0_0/ncbi_cxx--7_0_0.tar.gz
 # uncompress
 cd ..
 tar xzvf ../downloads/ncbi_cxx--7_0_0.tar.gz
 cd ncbi_cxx--7_0_0
 # bulid
 ./configure --prefix=/share/apps/ngs-ccts/ncbi_cxx--7_0_0 --with-optimization --with-mt --with-dll
 make
 make install

Vicuna

download

 # download - by hand - requires registration
 cd /share/apps/ngs-ccts/downloads
 firefox http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna
 mv vicuna.zip vicuna.v1.2.zip
 # uncompress
 cd ..
 unzip downloads/vicuna.v1.2.zip  -x '__MACOSX/*'

configure & build

 cd /share/apps/ngs-ccts/VICUNA_v1.2/src
 # patch in NCBI C++ library path
 sed -i.orig -c -e 's|MYPATH=.*|MYPATH=/share/apps/ngs-ccts/ncbi_cxx--7_0_0|' Makefile
 # set NCBI C++ into LIB path
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/ngs-ccts/ncbi_cxx--7_0_0/lib
 # !! Waiting for NCBI to finish building
 make

build vicuna_analysis

 cd /share/apps/ngs-ccts/VICUNA_v1.2/scripts/vicuna_analysis
 make clean
 make all

Note: pre-built exe for Linux 64bit!

in the "executable" subdirectory! see [1] but I've had some trouble with it. Now using only built version.

V_FAT

Pre-requisits

• MUSCLE v3.8: /share/apps/galaxy/galaxy-tools/bin/muscle: MUSCLE v3.8.31
• R 2.9+: /share/apps/galaxy/galaxy-tools/bin/R: R version 2.13.0 (2011-04-13)
• Mosaik 2.1: /share/apps/ngs-ccts/MOSAIK_2.1.73-source/bin NgsCctsBuildMosaik
• GeneWise 2.2.0: /share/apps/ngs-ccts/wise2.2.0: NgsCctsGeneWise
  • export WISECONFIGDIR=/share/apps/ngs-ccts/wise2.2.0/wisecfg/
  • Caution: galaxy has GeneWise 1.0 - which may be in path!

V_FAT

• /share/apps/ngs-ccts/VfatSoftwarePackage
• configfile.txt - backup

 mv configfile.txt configfile.txt.orig

• configfile.txt - fill in paths

 # configfile.txt
 #
 # where VFAT is installed
 scriptpath = '/share/apps/ngs-ccts/VfatSoftwarePackage/'
 # ----------------------------------------------------------------
 # bin folder of the Mosaik distribution
 mosaikpath = '/share/apps/ngs-ccts/MOSAIK-2.1.73-source/bin/'
 # networkFile folder of your Mosaik distribution
 mosaiknetworkpath = '/share/apps/ngs-ccts/MOSAIK-2.1.73-source/networkFile/'
 # ----------------------------------------------------------------
 # samtools install path
 samtoolspath = '/share/apps/galaxy/galaxy-tools/bin/samtools/'
 # ----------------------------------------------------------------
 # Muscle 3.8 installation
 musclepath = '/share/apps/galaxy/galaxy-tools/bin/'
 # ----------------------------------------------------------------
 perlpath = '/usr/bin/perl'
 # ----------------------------------------------------------------
 # path for the binaries of your installation of wise2.2. It should
 # be in your wise2.2.0 folder under /src/bin/.
 genewisepath = '/share/apps/ngs-ccts/wise2.2.0/src/bin/'
 # path for config folder that is required by wise2.2. It
 # should be in your wise2.2.0 folder under /wisecfg/.
 genewisecfgpath = '/share/apps/ngs-ccts/wise2.2.0/wisecfg/'
 # ----------------------------------------------------------------
 # /share/apps/ngs-ccts/wise2.2.0/wisecfg
 Rpath = '/share/apps/galaxy/galaxy-tools/bin/'
 # ----------------------------------------------------------------
 # VICUNA/V-FAT species-specific reference data
 refDataPath = '/share/apps/ngs-ccts/VfatSoftwarePackage/ViralReferenceGenomes/'

• run script to copy all scripts from configfile.txt into *.pl (ick!)

 cd /share/apps/ngs-ccts/VfatSoftwarePackage
 # first clean up perl path in configPaths.pl
 sed -i.orig '1 s|^.*perl|#!'`which perl`'|' configPaths.pl; diff configPaths.pl configPaths.pl.orig
 # then run it
 ./configPaths.pl ./configfile.txt

• clean up #! lines & perms - the configPaths.pl leaves an (illegal) space in there

 # set to /usr/bin/perl
 sed -i.orig '1 s|^.*perl|#!'`which perl`'|' *.pl
 chmod +x *.pl

• fix incorrectly spelled argument in vfat.pl

 # inline patch 
 patch
 *** vfat.pl     2013-05-16 16:18:45.344425015 -0500
 --- vfat.pl.bak 2013-05-16 16:19:36.077461441 -0500
 ***************
 *** 52,58 ****
 
   GetOptions(
         "minlongcont=i"         => \$option{minlongcont},
 !       "mincontiglen=i"        => \$option{mincontiglen},
         "readfa=s"                      => \$option{readfa},
         "readq=s"                               => \$option{readq},
         "readfa2=s"                     => \$option{readfa2},
 --- 52,58 ----
 
   GetOptions(
         "minlongcont=i"         => \$option{minlongcont},
 !       "mincontlen=i"  => \$option{mincontlen},
         "readfa=s"                      => \$option{readfa},
         "readq=s"                               => \$option{readq},
         "readfa2=s"                     => \$option{readfa2},