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Add ~/bin as recommended location for nextflow executable

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Anthony Underwood 2021-04-22 12:02:11 +01:00 committed by GitHub
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1 changed files with 4 additions and 2 deletions
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docs/sanger.md
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@ -11,6 +11,8 @@ The latest version of Nextflow is not installed by default on the cluster. You w
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) - Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
Recommendation place to move the `nextflow` executable is `~/bin` so that it's in the `PATH`.
Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command. Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
Nextflow shouldn't run directly on the submission node but on a compute node. Nextflow shouldn't run directly on the submission node but on a compute node.
To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh` To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh`
@ -27,10 +29,10 @@ export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128' export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
export NXF_ANSI_LOG=false export NXF_ANSI_LOG=false
export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000" export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
export NXF_VER=21.03.0-edge export NXF_VER=21.04.0-edge
/path/to/your/install/nextflow run \ nextflow run \
/path/to/nf-core/pipeline/main.nf \ /path/to/nf-core/pipeline/main.nf \
-w /path/to/some/dir/work \ -w /path/to/some/dir/work \
-profile sanger \ -profile sanger \