software:alignment:tophat:2.0.3
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Table of Contents
tophat 2.0.3 installation
Depends on samtools
and boost
! Make sure those are installed first…
Unpack
tar zxf tophat-2.0.3.tar.gz cd tophat-2.0.3
Configure, compile and install
./configure --prefix=/export/apps/tophat/2.0.3 --with-boost=/export/apps/boost/1.47.0 --with-bam=/export/apps/samtools/0.1.18 make -j4 sudo make install
Prepare module file
Allow users to load support for tophat using the module system:
sudo mkdir -p /export/apps/modules/modulefiles/tophat
Create the module file, /export/apps/modules/modulefiles/tophat/2.0.3:
#%Module1.0 ##################################################################### ## ## cufflinks Modulefile ## by Alan Orth, a.orth@cgiar.org ## set version 2.0.3 set prefix /export/apps/cufflinks/${version} set exec_prefix ${prefix} set url "http://cufflinks.cbcb.umd.edu/" set msg "This module adds cufflinks v$version to various paths\n\ncufflinks Official Site: $url\n" proc ModulesHelp { } { puts stderr "$msg" } module-whatis "$msg" conflict cufflinks prepend-path PATH ${exec_prefix}/bin # cufflinks 1.0.3 was compiled against boost 1.47.0, make sure if can find boost! prepend-path LD_LIBRARY_PATH /export/apps/boost/1.47.0/lib # cufflinks depends on samtools, load the samtools module as well if { ![is-loaded samtools] } { module load samtools }
Test module file
module load cufflinks/2.0.0
software/alignment/tophat/2.0.3.1339576268.txt.gz · Last modified: 2012/06/13 08:31 by aorth