Celera-Assembler-Users

This is a patch file for Celera Assembler 8.3rc2 'runCA.pl' to run on a Cray system where a hybrid scheduling system, SLURM + ALPS, is in use. Celera 8.3rc2 does not come with SLURM support and Brett Whitty has done some work adding SLURM options to it:

   https://github.com/brettwhitty/bw-ca-tools

However, that patch is suitable for native SLURM. With hybrid SLURM + ALPS, there needs to be some more tweaks.

This patch is based on Brett Whitty's version and can be applied by

    patch runCA runCA_SLURM_ALPS_patch

where runCA is the original perl script from wgs.

If you have any questions, please email [email protected]

Testing

The patch has been tested in the following environement:

• Magnus supercomputer, Pawsey Supercomputing Centre
• Cray XC40, PrgEnv-gnu/5.2.82, gcc/4.8.2, craype-haswell
• SLURM slurm/14.11.8-pawsey-3
• Celera wgs/8.3rc2
• Data is Escherichia_coli_K12_MG1655, using uncorrected PacBio reads, with CA8.2

Testing scripts are included. First, download the sample ecoli sequence data and prepare for the run

    ./get_ecoli_test_data.sh

which will generate a file called ecoli-untrimed.frg for later use.

Then to run the trimming test, submit the following script by

    sbatch job_script_trim.slurm

where job_script_trim.slurm is

    #!/bin/bash -l
  	#SBATCH --nodes=1 
  	#SBATCH --partition=workq
  	#SBATCH --time=1:00:00
  	#SBATCH --export=NONE
  	#SBATCH --account=pawsey0001
  	
  	module swap PrgEnv-cray/5.2.82 PrgEnv-gnu
  	module load python wgs/8.3
  	# export PATH and PERL5LIB if necessary
  	# export PATH=/path/to/the/installed/runCA:$PATH 
  	# export PERL5LIB=/path/to/the/Exporter-Tiny/List-MoreUtils/Statistics-Descriptive/perl/modules:$PERL5LIB

  	runCA -p ecoli-trim -d ecoli-trim -s ecoli-trim.spec ecoli-untrimmed.frg

Lastly, the assembly test is submitted by

    sbatch job_script_assembly.slurm

and the job script is

  	#!/bin/bash -l
  	#SBATCH --nodes=1 
  	#SBATCH --partition=workq
  	#SBATCH --time=1:00:00
  	#SBATCH --export=NONE
  	#SBATCH --account=pawsey0001
  	
  	module swap PrgEnv-cray/5.2.82 PrgEnv-gnu
  	module load python wgs/8.3
  	# export PATH and PERL5LIB if necessary
  	# export PATH=/path/to/the/installed/runCA:$PATH 
  	# export PERL5LIB=/path/to/the/Exporter-Tiny/List-MoreUtils/Statistics-Descriptive/perl/modules:$PERL5LIB

  	runCA -p ecoli-assembly -d ecoli-assembly -s ecoli-assembly.spec ecoli-untrimmed.frg