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wombat-p / WOMBAT-Pipelines

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Searchgui setup failing with singularity #11

Closed flevander closed 1 year ago

flevander commented 1 year ago

Description of the bug

When using the singularity profile, the workflow fails at the PREPARE_SEARCHGUI step. The error appears when trying to save the parameters file, despite the '--writable-tmpfs' singularity run option being enabled in nextflow.config.

Command used and terminal output

$ nextflow run main.nf --parameters test_params.yml --raws 'raws/*' --fasta uniprot_contaminant_yeast_ups_prot_03022023.fasta --sdrf sdrf_proline_ed.tsv -profile singularity

Relevant files

No response

System information

nextflow 23.04.2 build 5870 singularity-ce version 3.11.4-focal Ubuntu 22.04 wombat-pipelines 0.9.1

flevander commented 1 year ago

The specific error output is in COMPOMICS:PREPARE_SEARCHGUI

Command executed:

mkdir tmp mkdir log searchgui eu.isas.searchgui.cmd.PathSettingsCLI -temp_folder ./tmp -log ./log searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -out searchgui \ .....

Command output: An error occurred when saving the path preference to /usr/local/share/searchgui-4.2.9-0/resources/conf/paths.txt.

veitveit commented 1 year ago

I checked the docker container. There the respective folder is only writable by root. This could be issue.

As far as I oversee it now, the problem is that any change of user rights seem to be overwritten when installing the package via conda and then automatically making a docker container. We might need a specific container for searchgui and peptideshaker, where these rights are provided.

veitveit commented 1 year ago

This solved the issues when running with singularity:

This fixes work but are a bit dirty so far.

@flevander