Since many in the bioconda community enjoy helping out other researchers, I thought this would be a good place to post this job opportunity. This is an opening for Deputy Scientific Information Officer (appointed as Staff Scientist, a federal position), at the National Institute of Child Health and Human Development, National Institutes of Health in Bethesda, Maryland, USA. This is a multi-role position, including policy, process, strategy, governance, as well as technical aspects. Any questions please contact me by email (ryan.dale@nih.gov). Here's the ad: https://hpc.nih.gov/~dalerr/Deputy_SIO_NICHD.pdf.
Hello -- I am trying to update a package (RLPipes), but I seem to be running into an out-of-memory error (137) in the Azure build pipeline: https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=19658&view=logs&jobId=e14e69ff-a0ae-55c4-b71d-229b239cfb2f&j=e14e69ff-a0ae-55c4-b71d-229b239cfb2f&t=7df82132-b284-504b-53d6-7d3e63519572
Could anyone please advise on how to deal with this error?
Hello, I'm new to creating conda recipes. I'm planning to update my package bioconda (Autometa: https://anaconda.org/bioconda/autometa). However, I'm having an issue where one of the dependencies is only on pypi (gtdb-to-taxdump: https://pypi.org/project/gtdb-to-taxdump/). Is there a way to include this without the conda-build process attempting to install this via conda install?
@Sidduppal: You need to create a conda recipe for gtdb-to-taxdump first.
Done. @lcoombe please feel free to review and accept as well
1 reply
Anyone up for reviewing/merging three easy PRs for removing Perl packages migrated to conda-forge? bioconda/bioconda-recipes#36382 bioconda/bioconda-recipes#36309 bioconda/bioconda-recipes#36263
2 replies
Could anyone take a look at bioconda/bioconda-recipes#36395? Required checks are not initiating. Also, there are only two checks (test_linux and test_osx) instead of regular four (including lint).
Hello. I am trying to create a new recipe, and am trying to test it locally with bioconda-utils (I am on an intel Mac). When running with the --docker flag to test the linux build, I am getting this error:
18:12:29 BIOCONDA INFO (COMMAND) docker run -t --net host --rm -v /private/var/folders/7n/w898bvs90ks96x01g5s40w7w0000gn/T/tmp_pqferwt/build_script.bash:/opt/build_script.bash -v /usr/local/anaconda3/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /Users/andersgs/dev/andersgs/bioconda-recipes/recipes/phcue-ck:/opt/recipe -e LANG=en_US.UTF-8 -e HOST_USER_ID=501 quay.io/bioconda/bioconda-utils-build-env-cos7:1.0.1 /bin/bash /opt/build_script.bash
18:12:30 BIOCONDA INFO (OUT) mkdir: cannot create directory ‘/opt/host-conda-bld/linux-64’: Permission denied
18:12:30 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /private/var/folders/7n/w898bvs90ks96x01g5s40w7w0000gn/T/tmp_pqferwt/build_script.bash:/opt/build_script.bash -v /usr/local/anaconda3/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /Users/andersgs/dev/andersgs/bioconda-recipes/recipes/phcue-ck:/opt/recipe -e LANG=en_US.UTF-8 -e HOST_USER_ID=501 quay.io/bioconda/bioconda-utils-build-env-cos7:1.0.1 /bin/bash /opt/build_script.bash
18:12:30 BIOCONDA ERROR BUILD FAILED recipes/phcue-ck
18:12:30 BIOCONDA INFO (COMMAND) conda build purge
18:12:32 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
18:12:32 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/phcue-ckFor some reason the process is lacking sufficient permissions to create a folder. Has anyone come up against this issue too?
Thanks Ryan, there are three more if you have a minute.
1 reply
(and thanks Devon of course!)
Thanks; looks like feedstock conversion didn't work properly for that one, I'll prod some people.