1.3.1

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.

  1. 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
  1. 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
  1. 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

Author

  • Mateo Gómez Zuluaga