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modify alternative module load
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1 changed files with 4 additions and 2 deletions
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@ -13,7 +13,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using
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## Load Nextflow and Singularity environment modules
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## Load Nextflow and Singularity environment modules
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module purge
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module purge
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module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0
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module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0
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# alternative module load jdk/1.8.0_291 nextflow/22.04.3 singularity/3.8.0
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# alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0
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export NXF_OPTS='-Xms1g -Xmx4g'
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export NXF_OPTS='-Xms1g -Xmx4g'
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export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
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export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
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export NXF_TEMP=/scratch/tmp
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export NXF_TEMP=/scratch/tmp
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@ -26,7 +26,9 @@ mkdir $NXF_SINGULARITY_CACHEDIR
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mkdir $NXF_HOME
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mkdir $NXF_HOME
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```
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```
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finally download and test the pipeline of choice using the `-profile ku_sund_dangpu`
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Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the ku_sund_dangpu profile. Just make sure that the pipeline is run within a tmux session.
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```
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```
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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```
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```
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