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| anthill_sri011 [2019/07/06 12:59] – tmatejuk | anthill_sri011 [2023/08/01 01:08] (current) – external edit 127.0.0.1 | ||
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| ==== prepare software ==== | ==== prepare software ==== | ||
| - | Login to anthill23 and download rMATS along with some test dataset, and gft files: | + | Login to anthill23 and download rMATS along with some test datasets, and gft files((downloading this files will take about 3 minutes)): |
| @anthill23: | @anthill23: | ||
| Line 20: | Line 20: | ||
| wget ftp:// | wget ftp:// | ||
| gunzip Homo_sapiens.GRCh37.87.gtf.gz | gunzip Homo_sapiens.GRCh37.87.gtf.gz | ||
| - | wget ftp:// | ||
| - | gunzip Homo_sapiens.GRCh38.91.gtf.gz | ||
| ==== prepare gsl lib ==== | ==== prepare gsl lib ==== | ||
| - | rMATS uses gsl library that need to be prepared separately((takes about five minutes)). This library have to be compiled on computing node, so it is done in interactive mode ( | + | rMATS uses gsl library that need to be prepared separately((takes about five minutes)). This library have to be compiled on computing node, so it is done in interactive mode ([[howtouseslurm_000|SLURM, |
| - | [[howtouseslurm_000|SLURM, | + | |
| @anthill23: | @anthill23: | ||
| | | ||
| - | srun -N1 -n4 --pty bash -l | + | srun -J gsl_compile |
| | | ||
| cd ~/ | cd ~/ | ||
| Line 41: | Line 38: | ||
| cd ~/ | cd ~/ | ||
| ln -s libgsl.so libgsl.so.0 | ln -s libgsl.so libgsl.so.0 | ||
| - | + | ||
| + | exit | ||
| + | ==== simple test ==== | ||
| + | If above steps ( prepare software, and prepare gsl lib ) finish successfully this simple test should finish with success. Do this test in interactive mode ([[howtouseslurm_000|SLURM, | ||
| + | @anthill23: | ||
| + | | ||
| + | srun -J rMATS_test --pty bash -l | ||
| + | | ||
| + | cd / | ||
| + | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ | ||
| + | python rMATS.4.0.2/ | ||
| + | | ||
| + | ... | ||
| + | #read output and exit interactive mode when finished | ||
| + | exit | ||
| ==== sbatch example ==== | ==== sbatch example ==== | ||
| - | ... | + | Bellow example was taken form [[http:// |
| - | < | + | File '' |
| - | ... | + | |
| - | </ | + | |
| - | + | ||
| - | + | ||
| - | ==== performance tests ==== | + | |
| - | ... | + | |
| < | < | ||
| - | ... | ||
| - | </ | ||
| - | |||
| - | ---- | ||
| - | FIXME | ||
| - | |||
| - | < | ||
| - | |||
| - | 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:// | ||
| - | 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 ~/ | ||
| - | cd ~/ | ||
| - | git clone https:// | ||
| - | cd htslib | ||
| - | autoheader | ||
| - | autoconf | ||
| - | ./configure --prefix=/ | ||
| - | make -j ${SLURM_NTASKS} | ||
| - | make install | ||
| - | |||
| - | Then to prepare samtools run following commands ( it will take less than 4 minutes ) : | ||
| - | |||
| - | mkdir -p ~/ | ||
| - | cd ~/ | ||
| - | git clone https:// | ||
| - | cd samtools | ||
| - | autoheader | ||
| - | autoconf -Wno-syntax | ||
| - | ./configure --prefix=/ | ||
| - | make -j ${SLURM_NTASKS} | ||
| - | make install | ||
| - | |||
| - | Then to prepare bcftools run following commands ( it will take less than 3 minutes ) : | ||
| - | |||
| - | mkdir -p ~/ | ||
| - | cd ~/ | ||
| - | git clone https:// | ||
| - | cd bcftools | ||
| - | autoheader | ||
| - | autoconf | ||
| - | ./configure --prefix=/ | ||
| - | make -j ${SLURM_NTASKS} | ||
| - | make install | ||
| - | |||
| - | As a result samtools and bcftools binares will be located at : | ||
| - | |||
| - | / | ||
| - | / | ||
| - | |||
| - | batch file template | ||
| - | |||
| - | First login to anthill23.cent1.uw.edu.pl. | ||
| - | |||
| - | Then create job file (batch), and save it as i.e. samtools_testrun.batch . | ||
| - | |||
| #!/bin/bash -l | #!/bin/bash -l | ||
| - | #SBATCH --job-name=samtools_test | + | #SBATCH --partition=test |
| - | #SBATCH --partition=long | + | #SBATCH --ntasks=4 |
| - | #SBATCH --ntasks=2 | + | #SBATCH --mem 4G |
| - | #SBATCH --mem 2048M | + | #SBATCH --job-name rMATS_test |
| - | #samtools and bcftools binary executable paths | + | cd / |
| - | SAMTOOLSBINPATH=/ | + | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: |
| - | BCFTOOLSBINPATH=/ | + | |
| - | #printout some info | + | python rMATS.4.0.2/ |
| - | echo " | + | --b1 b1.txt \ |
| - | echo "date: " `date` | + | --b2 b2.txt \ |
| - | echo " | + | --gtf gtf/ |
| + | --od bam_test \ | ||
| + | -t paired \ | ||
| + | | ||
| + | | ||
| + | | ||
| - | #run samtool | + | </code> |
| - | ${SAMTOOLSBINPATH}/samtools | + | |
| - | #run bcftool | + | ==== performance tests ==== |
| - | ${BCFTOOLSBINPATH}/ | + | None. At this time. |
| - | Then run created batch file ( value 60628 is jobID, it will be different in each job submission): | ||
| - | [anteater@anthill23 tests]$ 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. | ||
| - | |||
| - | </ | ||