NgsCctsBuildVicuna

= Build/Install Broad's Vicuna =

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 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 mv configfile.txt configfile.txt.orig # 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/' 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 # set to /usr/bin/perl sed -i.orig '1 s|^.*perl|#!'`which perl`'|' *.pl chmod +x *.pl patch < vfat.pl.mincontlen.patch
 * /share/apps/ngs-ccts/VfatSoftwarePackage
 * configfile.txt - backup
 * configfile.txt - fill in paths
 * run script to copy all scripts from configfile.txt into *.pl (ick!)
 * clean up #! lines & perms - the configPaths.pl leaves an (illegal) space in there
 * fix incorrectly spelled argument in vfat.pl
 * 1) inline patch