software:alignment:tophat:2.0.3
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 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 ##################################################################### ## ## tophat Modulefile ## by Alan Orth, <a.orth@cgiar.org> ## June 13, 2012 ## set version 2.0.3 set appname tophat set prefix /export/apps/${appname}/${version} set exec_prefix ${prefix}/bin set datarootdir ${prefix}/share set url "http://tophat.cbcb.umd.edu" set msg "This module adds tophat v$version to various paths\n\ntophat Official Site: $url\n" proc ModulesHelp { } { puts stderr "$msg" } module-whatis "$msg" conflict tophat prepend-path PATH ${exec_prefix} prepend-path MANPATH ${datarootdir}/man # tophat depends on samtools, load the samtools module as well if { ![is-loaded samtools] } { module load samtools } # tophat depends on bowtie, load the bowtie module as well if { ![is-loaded bowtie] } { module load bowtie }
Test module file
module load tophat/2.0.3
software/alignment/tophat/2.0.3.txt · Last modified: 2012/06/13 08:41 by aorth