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Warning
titleSubmit to the TACC queue or run in an idev shell

Create a commands file and use launcher_creator.py followed by sbatch.

Expand

nano commands.star


Put this in your commands file:

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq

apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794488_C2_R3_1.fq ../data/GSM794488_C2_R3_2.fq


Expand
titleUse this Launcher_creator command

launcher_creator.py -j commands.star -n starmap -q normal -t 08:00:00 -a OTH21164 -l star_launcher.slurm -m "module load intel/17.0.4biocontainers; module load star" -N 6 -w 1


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