James: Text replacement - "[pP][bB][sS]" to "SLURM"

2022-10-20T20:36:56Z

Text replacement - "[pP][bB][sS]" to "SLURM"

← Older revision		Revision as of 20:36, 20 October 2022
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	utilities for extracting, reformatting, and displaying nucleotide sequences. The primary tool is called 'samtools'		utilities for extracting, reformatting, and displaying nucleotide sequences. The primary tool is called 'samtools'
	and offers a large number of command-line options. For smaller tasks, SAMTOOLS can be run interactively,		and offers a large number of command-line options. For smaller tasks, SAMTOOLS can be run interactively,
	but should be run in ~~PBS~~ batch mode when larger, longer tasks are anticipated. NOTE: that display tasks		but should be run in SLURM batch mode when larger, longer tasks are anticipated. NOTE: that display tasks
	cannot be run in pure ~~PBS~~ batch mode because the output is displayed. Larger display tasks should be		cannot be run in pure SLURM batch mode because the output is displayed. Larger display tasks should be
	run in ~~PBS~~ interactive mode as described in the ~~PBS~~ section elsewhere in this document.		run in SLURM interactive mode as described in the SLURM section elsewhere in this document.

	Below is an example ~~PBS~~ script that will convert the 'toy.sam' file provided with the distribution from		Below is an example SLURM script that will convert the 'toy.sam' file provided with the distribution from
	SAM to BAM format. This and all the example files can be copied from the local installation directory		SAM to BAM format. This and all the example files can be copied from the local installation directory
	to your current location as follows:		to your current location as follows:
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	Running 'samtools' from the interactive prompt without any options will provide a brief description of the form of the		Running 'samtools' from the interactive prompt without any options will provide a brief description of the form of the
	command-line argument and options. Here is ~~PBS~~ batch script that does a short format conversion in batch mode:		command-line argument and options. Here is SLURM batch script that does a short format conversion in batch mode:

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
	#~~PBS~~ -q production		#SLURM -q production
	#~~PBS~~ -N SAMTLS_serial		#SLURM -N SAMTLS_serial
	#~~PBS~~ -l select=1:ncpus=1:mem=2880mb		#SLURM -l select=1:ncpus=1:mem=2880mb
	#~~PBS~~ -l place=free		#SLURM -l place=free
	#~~PBS~~ -V		#SLURM -V

	# Find out name of master execution host (compute node)		# Find out name of master execution host (compute node)
	echo -n ">>>> ~~PBS~~ Master compute node is: "		echo -n ">>>> SLURM Master compute node is: "
	hostname		hostname

	# You must explicitly change to the working directory in ~~PBS~~		# You must explicitly change to the working directory in SLURM
	cd $~~PBS_O_WORKDIR~~		cd $SLURM_O_WORKDIR

	# Point to the execution directory to run		# Point to the execution directory to run
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	</pre>		</pre>

	Running this conversion test case should take less than 1 minutes and will produce ~~PBS~~ output and error files beginning with		Running this conversion test case should take less than 1 minutes and will produce SLURM output and error files beginning with
	the job name 'SAMTLS_serial'. The primary SAMTOOLS application results will be written into the user-specified file at the end		the job name 'SAMTLS_serial'. The primary SAMTOOLS application results will be written into the user-specified file at the end
	of the TOPHAT command line after the greater-than sign. Here it is named 'toy.bam' The expression '2 > toy.err' at the end		of the TOPHAT command line after the greater-than sign. Here it is named 'toy.bam' The expression '2 > toy.err' at the end
	of the command-line directs Unix standard error to the file 'toy.err'. Users should always explicitly specify the name of the		of the command-line directs Unix standard error to the file 'toy.err'. Users should always explicitly specify the name of the
	application's output files to ensure that they are written directly into the user's working directory which has much more disk		application's output files to ensure that they are written directly into the user's working directory which has much more disk
	space than the ~~PBS~~ spool directory on /var.		space than the SLURM spool directory on /var.

	Details on the meaning of the ~~PBS~~ script are covered below in the ~~PBS~~ section. The most important lines are the '#~~PBS~~ -l select=1:ncpus=1:mem=2880mb'		Details on the meaning of the SLURM script are covered below in the SLURM section. The most important lines are the '#SLURM -l select=1:ncpus=1:mem=2880mb'
	and the '#~~PBS~~ -l pack=free' lines. The first instructs ~~PBS~~ to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs		and the '#SLURM -l pack=free' lines. The first instructs SLURM to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs
	of memory in it for the job. The second instructs ~~PBS~~ to place this job on the least buy node where the requested resources		of memory in it for the job. The second instructs SLURM to place this job on the least buy node where the requested resources
	can be found (freely). The master compute node that ~~PBS~~ finally selects to run your job will be printed in the ~~PBS~~ output file		can be found (freely). The master compute node that SLURM finally selects to run your job will be printed in the SLURM output file
	by the 'hostname' command.		by the 'hostname' command.

James: Created page with "SAMTOOLS is part of a sequence alignment and analysis tool chain developed at John Hopkins, University of California at Berkeley, and Harvard, and distributed through the Center for Bioinformatics and Computational Biology. The other tools in this collection, BOWTIE, CUFFLINKS, and TOPHAT are also installed at the CUNY HPC Center. Additional information can be found at the SAMTOOLS home page here [http://samtools.sourceforge.net/index.shtml]. At the CUNY HPC Center S..."

2022-10-20T20:19:22Z

Created page with "SAMTOOLS is part of a sequence alignment and analysis tool chain developed at John Hopkins, University of California at Berkeley, and Harvard, and distributed through the Center for Bioinformatics and Computational Biology. The other tools in this collection, BOWTIE, CUFFLINKS, and TOPHAT are also installed at the CUNY HPC Center. Additional information can be found at the SAMTOOLS home page here [http://samtools.sourceforge.net/index.shtml]. At the CUNY HPC Center S..."

New page

SAMTOOLS is part of a sequence alignment and analysis tool chain developed at John Hopkins, University
of California at Berkeley, and Harvard, and distributed through the Center for Bioinformatics and Computational
Biology. The other tools in this collection, BOWTIE, CUFFLINKS, and TOPHAT are also installed at the CUNY
HPC Center. Additional information can be found at the SAMTOOLS home page here [http://samtools.sourceforge.net/index.shtml].

At the CUNY HPC Center SAMTOOLS is installed on ANDY. SAMTOOLS is a collection of
utilities for extracting, reformatting, and displaying nucleotide sequences. The primary tool is called 'samtools'
and offers a large number of command-line options. For smaller tasks, SAMTOOLS can be run interactively,
but should be run in PBS batch mode when larger, longer tasks are anticipated. NOTE: that display tasks
cannot be run in pure PBS batch mode because the output is displayed. Larger display tasks should be
run in PBS interactive mode as described in the PBS section elsewhere in this document.

Below is an example PBS script that will convert the 'toy.sam' file provided with the distribution from
SAM to BAM format. This and all the example files can be copied from the local installation directory
to your current location as follows:

<pre>
cp /share/apps/samtools/default/examples/* .
</pre>

To include all required environmental variables and the path to the SAMTOOLS executables run the modules
load command (the modules utility is discussed in detail above):

<pre>
module load samtools
</pre>

Running 'samtools' from the interactive prompt without any options will provide a brief description of the form of the
command-line argument and options. Here is PBS batch script that does a short format conversion in batch mode:

<pre>
#!/bin/bash
#PBS -q production
#PBS -N SAMTLS_serial
#PBS -l select=1:ncpus=1:mem=2880mb
#PBS -l place=free
#PBS -V

# Find out name of master execution host (compute node)
echo -n ">>>> PBS Master compute node is: "
hostname

# You must explicitly change to the working directory in PBS
cd $PBS_O_WORKDIR

# Point to the execution directory to run
echo ">>>> Begin SAMTLS Serial Run ..."
samtools view -bS toy.sam > toy.bam 2 > toy.err
echo ">>>> End SAMTLS Serial Run ..."
</pre>

This script can be dropped in to a file (say samtools_ser.job) and started with the command:

<pre>
qsub samtools_ser.job
</pre>

Running this conversion test case should take less than 1 minutes and will produce PBS output and error files beginning with
the job name 'SAMTLS_serial'. The primary SAMTOOLS application results will be written into the user-specified file at the end
of the TOPHAT command line after the greater-than sign. Here it is named 'toy.bam' The expression '2 > toy.err' at the end
of the command-line directs Unix standard error to the file 'toy.err'. Users should always explicitly specify the name of the
application's output files to ensure that they are written directly into the user's working directory which has much more disk
space than the PBS spool directory on /var.

Details on the meaning of the PBS script are covered below in the PBS section. The most important lines are the '#PBS -l select=1:ncpus=1:mem=2880mb'
and the '#PBS -l pack=free' lines. The first instructs PBS to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs
of memory in it for the job. The second instructs PBS to place this job on the least buy node where the requested resources
can be found (freely). The master compute node that PBS finally selects to run your job will be printed in the PBS output file
by the 'hostname' command.

SAMTOOLS - Revision history

James: Text replacement - "[pP][bB][sS]" to "SLURM"