Difference between revisions of "RNAFramework Job Scripts"
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Johnbullard (talk | contribs) (Created page with "Return to RNAFramework main page == Job script used for testing application installation == <pre> #!/bin/bash #SBATCH --job-name=rnaframework_2.7.2_test #SBA...") |
Johnbullard (talk | contribs) (Modified test with a customer-provided (smaller) dataset and workflow) |
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| Line 28: | Line 28: | ||
################################### | ################################### | ||
| − | echo 'Retrieving reference index...' | + | # echo 'Retrieving reference index...' |
| − | rf-index \ | + | # rf-index \ |
| − | --prebuilt 6 \ | + | # --prebuilt 6 \ |
| − | --bowtie2 \ | + | # --bowtie2 \ |
| − | --processors ${SLURM_CPUS_ON_NODE:-1} | + | # --processors ${SLURM_CPUS_ON_NODE:-1} |
echo 'Map reads to reference...' | echo 'Map reads to reference...' | ||
| Line 38: | Line 38: | ||
--bowtie2 \ | --bowtie2 \ | ||
--processors ${SLURM_CPUS_ON_NODE:-1} \ | --processors ${SLURM_CPUS_ON_NODE:-1} \ | ||
| − | - | + | --mapping-params "-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 "\ |
| − | + | --bowtie-index ${TEST_DATADIR}/reference/reference ${TEST_DATADIR}/571-2_S2_L003_R2_001.fastq | |
| − | |||
| − | - | ||
echo 'Count RT-stops in both samples...' | echo 'Count RT-stops in both samples...' | ||
rf-count \ | rf-count \ | ||
--processors ${SLURM_CPUS_ON_NODE:-1} \ | --processors ${SLURM_CPUS_ON_NODE:-1} \ | ||
| − | + | --fasta ${TEST_DATADIR}/reference/reference.fa \ | |
| − | --fasta | + | rf_map/571-2_S2_L003_R2_001.bam |
| − | rf_map/ | ||
echo 'Normalize data...' | echo 'Normalize data...' | ||
rf-norm \ | rf-norm \ | ||
--processors ${SLURM_CPUS_ON_NODE:-1} \ | --processors ${SLURM_CPUS_ON_NODE:-1} \ | ||
| − | -- | + | --scoring-method 4 \ |
| − | -- | + | --raw \ |
| − | -- | + | --treated rf_count/571-2_S2_L003_R2_001.rc |
| − | echo 'Perform inference of secondary structures...' | + | # echo 'Perform inference of secondary structures...' |
| − | rf-fold \ | + | # rf-fold \ |
| − | --processors ${SLURM_CPUS_ON_NODE:-1} \ | + | # --processors ${SLURM_CPUS_ON_NODE:-1} \ |
| − | -img \ | + | # -img \ |
| − | S1_vs_V1_norm | + | # S1_vs_V1_norm |
################################### | ################################### | ||
# There should be some files in the work directory | # There should be some files in the work directory | ||
echo "There should be some results listed below:" | echo "There should be some results listed below:" | ||
| − | find ${TEST_WORKDIR}/rf_fold -type f ! -empty -ls | + | find ${TEST_WORKDIR}/571-2_S2_L003_R2_001_raw f ! -empty -ls |
| + | #find ${TEST_WORKDIR}/rf_fold -type f ! -empty -ls | ||
echo "Test complete at $(date)." | echo "Test complete at $(date)." | ||
</pre> | </pre> | ||
Latest revision as of 16:33, 14 April 2022
Return to RNAFramework main page
Job script used for testing application installation
#!/bin/bash
#SBATCH --job-name=rnaframework_2.7.2_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=24:00:00
#SBATCH --output=rnaframework_2.7.2_test.log
echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/rnaframework/2.7.2
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output
cd ${TEST_PWD}
module load rnaframework/2.7.2
# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}
cd ${TEST_WORKDIR}
echo "Starting test run at $(date) on $(hostname)..."
###################################
# echo 'Retrieving reference index...'
# rf-index \
# --prebuilt 6 \
# --bowtie2 \
# --processors ${SLURM_CPUS_ON_NODE:-1}
echo 'Map reads to reference...'
rf-map \
--bowtie2 \
--processors ${SLURM_CPUS_ON_NODE:-1} \
--mapping-params "-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 "\
--bowtie-index ${TEST_DATADIR}/reference/reference ${TEST_DATADIR}/571-2_S2_L003_R2_001.fastq
echo 'Count RT-stops in both samples...'
rf-count \
--processors ${SLURM_CPUS_ON_NODE:-1} \
--fasta ${TEST_DATADIR}/reference/reference.fa \
rf_map/571-2_S2_L003_R2_001.bam
echo 'Normalize data...'
rf-norm \
--processors ${SLURM_CPUS_ON_NODE:-1} \
--scoring-method 4 \
--raw \
--treated rf_count/571-2_S2_L003_R2_001.rc
# echo 'Perform inference of secondary structures...'
# rf-fold \
# --processors ${SLURM_CPUS_ON_NODE:-1} \
# -img \
# S1_vs_V1_norm
###################################
# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/571-2_S2_L003_R2_001_raw f ! -empty -ls
#find ${TEST_WORKDIR}/rf_fold -type f ! -empty -ls
echo "Test complete at $(date)."