Vertebrate Alternative Splicing and Transcription Tools (VAST-TOOLS) is a toolset for profiling and comparing alternative splicing events in RNA-Seq data. It is particularly suited for evolutionary comparisons.
https://github.com/vastgroup/vast-tools
- Module Name: vasttools (see the modules page for more information)
- Programs are multithreaded (use -c flag).
- Databases are under /fdb/VASTDB
- Example files are under /usr/local/apps/vasttools/SRR7802623.fastq
Allocate an interactive session and run the interactive job there.
[biowulf]$ sinteractive --mem=10g --cpus-per-task=4 salloc.exe: Granted job allocation 789523 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn0135 are ready for job [cn0135]$ cd /data/$USER/ [cn0135]$ module load vasttools [cn0135]$ cp /usr/local/apps/vasttools/SRR7802623 [cn0135]$ vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out [cn0135]$ exit salloc.exe: Job allocation 789523 has been revoked. [biowulf]$
Note: this job allocates 10 GB of memory and automatically assign the number of cpus allocated (4 in this case) to the variable $SLURM_CPUS_PER_TASK.
1. Create a script file (myscript) similar to the one below.
#!/bin/bash cd /data/$USER/testData module load vasttools vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out
2. Submit the script on biowulf:
[biowulf]$ sbatch --mem=10g --cpus-per-task=4 myscript
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/$USER/cmdfile).
cd /data/$USER/dir1; vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out cd /data/$USER/dir2; vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out cd /data/$USER/dir3; vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out ... cd /data/$USER/dir20; vast-tools align SRR7802623.fastq -sp Hsa -c $SLURM_CPUS_PER_TASK --expr -o out
submit the swarm job:
$ swarm -f cmdfile --module hint -g 10 -t 4
For more information regarding running swarm, see swarm.html