Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • 15:42
    kstangline edited #36436
  • 15:41
    kstangline edited #36436
  • 15:30
    cbrueffer labeled #36437
  • 15:30
    cbrueffer opened #36437
  • 15:20
    kstangline edited #36436
  • 15:19
    kstangline opened #36436
  • 14:58
    daler synchronize #36229
  • 14:57
    cbrueffer labeled #36435
  • 14:57
    cbrueffer opened #36435
  • 14:51
    BiocondaBot commented #36255
  • 14:49
    daler commented #36255
  • 14:47
    cbrueffer labeled #36434
  • 14:47
    daler labeled #36289
  • 14:47
    cbrueffer opened #36434
  • 14:47
    daler labeled #36284
  • 14:34
    cbrueffer labeled #36433
  • 14:34
    cbrueffer opened #36433
  • 14:32
    daler synchronize #36229
  • 14:29
    andersgs review_requested #36399
  • 14:29
    andersgs review_requested #36399
Ryan Dale
@daler
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.
Jared Lumpe
@jlumpe
Is it possible to change the name of an existing recipe?
4 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36256
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36257
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36256
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36252
karl-az
@karl-az
Henry Miller
@millerh1

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?

Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36276
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36264
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36278
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36279
Devon Ryan
@dpryan79
@millerh1 Try restricting the dependency versions in the recipe inside the run: section.
2 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36288
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36287
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36293
Siddharth Uppal
@Sidduppal
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?
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36298
Nicola Soranzo
@nsoranzo:matrix.org
[m]
@Sidduppal: You need to create a conda recipe for gtdb-to-taxdump first.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36304
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36316
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36332
Lauren Coombe
@lcoombe
Hello! Would it be possible to review and merge this PR: bioconda/bioconda-recipes#36305 Thank you!
bgruening
@bgruening:matrix.org
[m]
Done. @lcoombe please feel free to review and accept as well
1 reply
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36318
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36327
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36353
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36357
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36354
Lucille Delisle
@lldelisle
Dear Bioconda team,
Is there a way to write a recipe and force the dependency to be:
fiji>=20220414 but not built h527b516_0 nor h9ee0642_0
?
Thanks
3 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36358
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36366
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36372
Christian Brueffer
@cbrueffer:matrix.org
[m]
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
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36375
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36297
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36385
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36389
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36370
Seung-been "Steven" Lee
@sbslee
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).
Anders Goncalves da Silva
@andersgs

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-ck

For some reason the process is lacking sufficient permissions to create a folder. Has anyone come up against this issue too?

Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36395
Devon Ryan
@dpryan79
@andersgs That path is the same as /usr/local/anaconda3/envs/bioconda/conda-bld/linux-64, which I suspect your users doesn't have write permissions to. Alternatively you can precreate that directory and make sure everyone has write permissions.
2 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36396
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36389
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36409
Christian Brueffer
@cbrueffer:matrix.org
[m]
Thanks Ryan, there are three more if you have a minute.
1 reply
(and thanks Devon of course!)
Christian Brueffer
@cbrueffer:matrix.org
[m]
Thanks; looks like feedstock conversion didn't work properly for that one, I'll prod some people.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#36399