CRwiki

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software

Tools (written in C using htslib) for manipulating next-generation sequencing data. The original samtools package has been split into three separate but tightly coordinated projects:

    htslib: C-library for handling high-throughput sequencing data
    samtools: mpileup and other tools for handling SAM, BAM, CRAM
    bcftools: calling and other tools for handling VCF, BCF

Software and its description is available at : https://github.com/samtools/samtools
software instalation @anthill23

Before you can use samtools tools at anthill you need to install it.

Firstly login to anthill23.cent1.uw.edu.pl and open an interactive session :

srun -p short --pty bash -l

Then to prepare htslib run following commands (it will take less than 3 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/htslib
cd htslib
autoheader
autoconf
./configure --prefix=/home/users/${USER}/anthill23_soft/samtools/htslib
make -j ${SLURM_NTASKS}
make install

Then to prepare samtools run following commands ( it will take less than 4 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/samtools.git
cd samtools
autoheader
autoconf -Wno-syntax
./configure --prefix=/home/users/${USER}/anthill23_soft/samtools
make -j ${SLURM_NTASKS}
make install

Then to prepare bcftools run following commands ( it will take less than 3 minutes ) :

mkdir -p ~/anthill23_soft/samtools
cd ~/anthill23_soft/samtools
git clone https://github.com/samtools/bcftools.git
cd bcftools
autoheader
autoconf
./configure --prefix=/home/users/${USER}/anthill23_soft/bcftools
make -j ${SLURM_NTASKS}
make install

As a result samtools and bcftools binares will be located at :

/home/users/${USER}/anthill23_soft/samtools/bin
/home/users/${USER}/anthill23_soft/bcftools/bin

batch file template

First login to anthill23.cent1.uw.edu.pl.

Then create job file (batch), and save it as i.e. samtools_testrun.batch .

#!/bin/bash -l
#SBATCH --job-name=samtools_test
#SBATCH --partition=long
#SBATCH --ntasks=2
#SBATCH --mem 2048M

#samtools and bcftools binary executable paths
SAMTOOLSBINPATH=/home/users/${USER}/anthill23_soft/samtools/bin
BCFTOOLSBINPATH=/home/users/${USER}/anthill23_soft/bcftools/bin

#printout some info
echo "samtools at anthill test"
echo "date: " `date`
echo "node_name: " `hostname`

#run samtool
${SAMTOOLSBINPATH}/samtools

#run bcftool
${BCFTOOLSBINPATH}/bcftools

Then run created batch file ( value 60628 is jobID, it will be different in each job submission):

[anteater@anthill23 tests]$ sbatch star_testrun.batch
Submitted batch job 60634

Depending on availability of computing nodes your job should end in just few moments, and batch output will be located in slurm-60634.out file.