From UABgrid Documentation
Revision as of 02:53, 28 March 2013 by Curtish@uab.edu
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
# 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
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.
- 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!