Table of Contents
1.3.1¶
- Installation date: 28/02/2017
- URL: http://samtools.sourceforge.net/
- Apolo version: Apolo II
- License: The MIT/Expat License
Dependencies¶
- Intel Parallel Studio XE Cluster Edition 2017 Update 1
- zlib >= 1.2.11
Installation¶
After solving the aforementioned dependencies, you can proceed with the installation of SAMtools.
- Download the latest version of the software (Source code - bz2) (https://sourceforge.net/projects/samtools/files/):
cd /home/$USER/apps/samtools/src
wget https://downloads.sourceforge.net/project/samtools/samtools/1.3.1/samtools-1.3.1.tar.bz2?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsamtools%2Ffiles%2Fsamtools%2F&ts=1488295734&use_mirror=ufpr
tar xf samtools-1.3.1.tar.bz2
- For configuration and compilation, the following steps must be taken:
cd samtools-1.3.1
module load zlib/1.2.11_intel-2017_update-1
./configure --prefix=/share/apps/samtools/1.3.1/intel/2017_update-1 2>&1 conf-samtools.log
make 2>&1 | tee make-samtools.log
make check 2>&1 | tee make-check-samtools.log
- After compiling SAMtools, we continue with the following steps:
sudo mkdir -p /share/apps/samtools/1.3.1/intel/2017_update-1
sudo mkdir -p /share/apps/samtools/1.3.1/intel/2017_update-1/include/bam
sudo mkdir -p /share/apps/samtools/1.3.1/intel/2017_update-1/lib
sudo chown -R $USER.apolo /share/apps/samtools/1.3.1/intel/2017_update-1
make install 2>&1 | tee make-install-samtools.log
cp libbam.a /share/apps/bwa/0.7.15/intel/2017_update-1/lib
cp *.h /share/apps/samtools/1.3.1/intel/2017_update-1/include/bam
sudo chown -R root.root /share/apps/samtools/1.3.1/intel/2017_update-1
Module¶
#%Module1.0#####################################################################
##
## module load samtools/1.3.1_intel-2017_update-1
##
## /share/apps/modules/samtools/1.3.1_intel-2017_update-1 Written by Mateo Gomez-Zuluaga
##
proc ModulesHelp { } {
puts stderr "\tsamtools/1.3.1 - sets the Environment for SAMTOOLS in \
\n\tthe share directory /share/apps/samtools/1.3.1/intel-2017_update-1\n"
}
module-whatis "\n\n\tSets the environment for using SAMTOOLS-1.3.1 \
\n\tbuilded with Intel Parallel Studio XE 2017\n"
# for Tcl script use only
set topdir /share/apps/samtools/1.3.1/intel/2017_update-1
set version 1.3.1
set sys x86_64-redhat-linux
module load intel/2017_update-1
prepend-path PATH $topdir/bin
prepend-path LD_LIBRARY_PATH $topdir/lib
prepend-path LIBRARY_PATH $topdir/lib
prepend-path LD_RUN_PATH $topdir/lib
prepend-path C_INCLUDE_PATH $topdir/include
prepend-path CXX_INCLUDE_PATH $topdir/include
prepend-path CPLUS_INCLUDE_PATH $topdir/include
prepend-path MANPATH $topdir/share/ma
Mode of use¶
Load the necessary environment through the module:
module load samtools/1.3.1_intel-2017_update-1
TO-DO
References¶
- INSTALL (File inside compressed package)
- https://github.com/cole-trapnell-lab/cufflinks