NgsCctsBuildVicuna
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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.