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Scripture on Biowulf

Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail scripture
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
scripture

$ module load scripture

$ module list
Currently Loaded Modulefiles:
1) scripture $ module unload scripture $ module show scripture # this actually show graphviz module since it's used to view output of scripture. ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/scripture: module-whatis Sets up graphviz v2.28 prepend-path PATH /usr/local/graphviz-2.28.0_el5/bin prepend-path LD_LIBRARY_PATH /usr/local/graphviz-2.28.0_el5/ -----------------------------------------------------------------

Submitting a single batch job

1. Create a script file alone the following lines.

#!/bin/bash
# This file is YourOwnFileName
#
#PBS -N yourownfilename
#PBS -m be
#PBS -k oe
module load scripture
java -jar /usr/local/scripture-beta2.jar ...........
[......]

2. Submit the script using the 'qsub' command on Biowulf.

$ qsub -l nodes=1 /data/$USER/theScriptFileAbove

 

Submitting a swarm of jobs

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). Here is a sample file:

module load scripture; cd /data/user/run1/;scripture command 1; scripture command 2
module load scripture; cd /data/user/run2/; scripture command 1; scripture command 2
........
........

 

There are one flag of swarm that's required '-f'.

-f: the swarm command file name above (required)

By default, each line of the commands above will be executed on '1' processor core of a node and uses 1GB of memory. If this is not what you want, you will need to specify '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

$ swarm -g 10 -f cmdfile

For more information regarding running swarm, see swarm.html

 

Running an interactive job

User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

$ qsub -I -l nodes=1
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready
$ module load scripture
$ scripture command 1
$ scripture command 2
$ ...........
$ exit
qsub: job 2236960.biobos completed
$

User may add property of node in the qsub command to request specific interactive node. For example, if you need a node with 8gb of memory to run job interactively, do this:

[user@biowulf]$ qsub -I -l nodes=1:g8

 

Documentation

http://www.broadinstitute.org/software/scripture/Walkthrough_example