====== 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,
## 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