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NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.
GNU General Public License v3.0
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PBS script not loading conda #29

Closed ViriatoII closed 4 years ago

ViriatoII commented 4 years ago

Hi,

The .command.run that is generated in my scratch does not load conda and then fails to find it. 

/var/spool/pbs/mom_priv/jobs/5865502.hpc-batch14.SC: line 286: conda: command not found
/var/spool/pbs/mom_priv/jobs/5865502.hpc-batch14.SC: line 286: /bin/activate: No such file or directory

In PBS, conda is not in PATH unless its loaded, in my case it's :

module load Miniconda/3 # but it might be different on other clusters

Is there a way of automatically integrating this in the .command.run file? Otherwise the solution is to put it in my .bashrc, I lost sometime before that occured to me.

mahesh-panchal commented 4 years ago

Hi @ViriatoII ,

There are several options available to you to resolve this if you've not been able to. You can use the module directive in a custom config to do module load Miniconda/3. There is also the beforeScript directive that lets you execute something before a script is run.

https://www.nextflow.io/docs/latest/process.html#module

I hope this solves your question. Regards