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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.

Code Block
titlePut this in your commands file
nano commands.hisat2

singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794483_C1_R1_1.fq -2 ../data/GSM794483_C1_R1_2.fq -S GSM794483_C1.sam --phred33 --novel-splicesite-outfile GSM794483_C1.junctions --rna-strandness RF --dta -t
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794484_C1_R2_1.fq -2 ../data/GSM794484_C1_R2_2.fq -S GSM794484_C1.sam --phred33 --novel-splicesite-outfile GSM794484_C1.junctions --rna-strandness RF --dta -t
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794485_C1_R3_1.fq -2 ../data/GSM794485_C1_R3_2.fq -S GSM794485_C1.sam --phred33 --novel-splicesite-outfile GSM794485_C1.junctions --rna-strandness RF --dta -t
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794486_C2_R1_1.fq -2 ../data/GSM794486_C2_R1_2.fq -S GSM794486_C1.sam --phred33 --novel-splicesite-outfile GSM794486_C1.junctions --rna-strandness RF --dta -t
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794487_C2_R2_1.fq -2 ../data/GSM794487_C2_R2_2.fq -S GSM794487_C1.sam --phred33 --novel-splicesite outfile GSM794487_C1.junctions --rna-strandness RF --dta -t
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2 -x ../reference/genome.fa -1 ../data/GSM794488_C2_R3_1.fq -2 ../data/GSM794488_C2_R3_2.fq -S GSM794488_C1.sam --phred33 --novel-splicesite-outfile GSM794488_C1.junctions --rna-strandness RF --dta -t


Expand
titleUse this Launcher_creator command

launcher_creator.py -n hisat2 -t 01:00:00 -j commands.hisat2 -q normal -a UT-2015-05-18 DNAdenovo -l hisat2_launcher.slurm -m " module load biocontainers; module load hisat2/ctr-2.1.0--py36pl5.22.0_0"


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