Installing timeout

[menegidio-lab]

I need to install Mitos locally and I see the error below:

(1/9) Installing repository mitos from iuc to section "annotate-mito" at revision f86bcffa9549 (TRT: 0:00:07.556675)
Timeout during install of mitos, extending wait to 1h

This error is seen for Mitos and Mitos2, however, other tools install normally. The error is viewed by both the server https://toolshed.g2.bx.psu.edu and https://testtoolshed.g2.bx.psu.edu

I've been trying to install for two consecutive days. I will need the tool for a workshop.

Currently the settings are:

api_key: admin
galaxy_instance: http: // localhost: 8080
install_repository_dependencies: True
install_resolver_dependencies: True
install_tool_dependencies: True
tools:

name: mitos
owner: iuc
tool_panel_section_id: 'annotate-mito'
tool_shed_url: https://toolshed.g2.bx.psu.edu/

name: mitos2
owner: iuc
tool_panel_section_id: 'annotate-mito'
tool_shed_url: https://toolshed.g2.bx.psu.edu

[bgruening]

install_repository_dependencies: False
install_resolver_dependencies: True
install_tool_dependencies: False

See here: https://github.com/usegalaxy-eu/usegalaxy-eu-tools/blob/master/imaging.yaml

But I assume its the R dependency. Which conda version are you using?

[menegidio-lab]

Galaxy 20.09
conda 4.10.1

[bgruening]

I assume it is this problem: bioconda/bioconda-recipes#13774

@menegidio-lab two tipps. If Galaxy/nginx times out, this is usually not a problem as the conda installation will still be running and finishing eventually. You could also create the env by hand and pin r-base=4 to speed up the solving process by conda.

Alternatively, we could pin an R version in he upstream mitos package. ping @bernt-matthias

[bernt-matthias]

Lets try bioconda/bioconda-recipes#28746 ..

[bernt-matthias]

Hmm. Even with R>=3 and R>=4 I get incompatibilities?

[bernt-matthias]

Do you have the chance to use docker / singularity?

[bernt-matthias]

solved by bioconda/bioconda-recipes#28746 .. @bgruening issue can be closed