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]
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
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