...
| Code Block |
|---|
|
module load biocontainers
module spider hisat2
module load python3/3.7.0
module load hisat2/ctr-2.1.0--py36pl5.22.0_0 |
| Code Block |
|---|
| title | Check is hisat2 is accessible after loading module |
|---|
|
hisat2 |
This doesn't work because when you load biocontainer (singularity) modules, it doesn't simply add the tool/executable to your path. Instead, it defines a function and you will needd to use that function definition to run the tool.
| Code Block |
|---|
| title | Get the function definition for hisat2 biocontainer module |
|---|
|
type hisat2 |
Part 1. Create a index of your reference
NO NEED TO RUN THIS NOW- YOUR INDEX HAS ALREADY BEEN BUILT!
| Code Block |
|---|
singularity exec ${BIOCONTAINER_DIR}/biocontainers/hisat2/hisat2-2.1.0--py36pl5.22.0_0.simg hisat2-build reference/genome.fa reference/genome.fa |
...
| Warning |
|---|
| title | Submit to the TACC queue or run in an idev shell |
|---|
|
Create a commands file and use launcher_creator.py followed by sbatch. | Code Block |
|---|
| title | Put 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 |
|---|
| title | Use this Launcher_creator command |
|---|
| launcher_creator.py -n hisat2 -t 01:00:00 -j commands.hisat2 -q normal -a UT-2015-05-18 -l hisat2_launcher.slurm -m " module load biocontainers; module load python3/3.7.0; module load hisat2/ctr-2.1.0--py36pl5.22.0_0" |
|
...