Differences

This shows you the differences between two versions of the page.

--- anthill_sri011 [2019/07/06 12:59] – tmatejuk
+++ anthill_sri011 [2023/08/01 01:08] (current) – external edit 127.0.0.1
@@ Line 6: / Line 6: @@
 ==== 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:~$
@@ Line 20: / Line 20: @@
   wget ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
   gunzip Homo_sapiens.GRCh37.87.gtf.gz
-  wget ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz
-  gunzip Homo_sapiens.GRCh38.91.gtf.gz
 ==== 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, batch and interactive mode]]) :
-[[howtouseslurm_000|SLURM, batch and interactive mode]]) :
   @anthill23:~$
-  srun -N1 -n4 --pty bash -l
+  srun -J gsl_compile -N1 -n4 --pty bash -l
   cd ~/anthill23_rmats/
@@ Line 41: / Line 38: @@
   cd ~/anthill23_rmats/gsl-2.4/lib
   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, batch and interactive mode]]) :
+  @anthill23:~$
+  srun -J rMATS_test --pty bash -l
+  cd /home/users/${USER}/anthill23_rmats
+  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib
+  python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 testData/b1.txt --b2 testData/b2.txt --gtf gtf/Homo_sapiens.GRCh37.87.gtf --od bam_test -t paired --readLength 50 --cstat 0.0001 --libType fr-unstranded
+  ...
+  #read output and exit interactive mode when finished
+  exit
 ==== sbatch example ====
-...
+Bellow example was taken form [[http://rnaseq-mats.sourceforge.net/user_guide.htm|rMATS User Guide]]. This description assumes that above steps ( prepare software, and prepare gsl lib ) were done beforehand if not, remember to modify them accordingly.
-<code>
+File ''rmats_test.batch'' .
-...
-</code>
-==== performance tests ====
-...
 <code>
-...
-</code>
-----
-FIXME
-<code>
-software
-Tools (written in C using htslib) for manipulating next-generation sequencing data. The original samtools package has been split into three separate but tightly coordinated projects:
-    htslib: C-library for handling high-throughput sequencing data
-    samtools: mpileup and other tools for handling SAM, BAM, CRAM
-    bcftools: calling and other tools for handling VCF, BCF
-Software and its description is available at : https://github.com/samtools/samtools
-software instalation @anthill23
-Before you can use samtools tools at anthill you need to install it.
-Firstly login to anthill23.cent1.uw.edu.pl and open an interactive session :
-srun -p short --pty bash -l
-Then to prepare htslib run following commands (it will take less than 3 minutes ) :
-mkdir -p ~/anthill23_soft/samtools
-cd ~/anthill23_soft/samtools
-git clone https://github.com/samtools/htslib
-cd htslib
-autoheader
-autoconf
-./configure --prefix=/home/users/${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/${USER}/anthill23_soft/bcftools/bin
-batch file template
-First login to anthill23.cent1.uw.edu.pl.
-Then create job file (batch), and save it as i.e. samtools_testrun.batch .
 #!/bin/bash -l
-#SBATCH --job-name=samtools_test
+#SBATCH --partition=test
-#SBATCH --partition=long
+#SBATCH --ntasks=4
-#SBATCH --ntasks=2
+#SBATCH --mem 4G
-#SBATCH --mem 2048M
+#SBATCH --job-name rMATS_test
-#samtools and bcftools binary executable paths
+cd /home/users/${USER}/anthill23_rmats
-SAMTOOLSBINPATH=/home/users/${USER}/anthill23_soft/samtools/bin
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib
-BCFTOOLSBINPATH=/home/users/${USER}/anthill23_soft/bcftools/bin
-#printout some info
+python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py \
-echo "samtools at anthill test"
+ --b1 b1.txt \
-echo "date: " `date`
+ --b2 b2.txt \
-echo "node_name: " `hostname`
+ --gtf gtf/Homo_sapiens.GRCh37.87.gtf \
+ --od bam_test \
+ -t paired \
+ --readLength 50 \
+ --cstat 0.0001 \
+ --libType fr-unstranded
-#run samtool
+</code>
-${SAMTOOLSBINPATH}/samtools
-#run bcftool
+==== performance tests ====
-${BCFTOOLSBINPATH}/bcftools
+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.
-</code>

CRwiki

User Tools

Site Tools

Differences

Page Tools