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Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25452
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25412
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25461
Jens Preu├čner
@jenzopr
Hi all! Is there a way to trigger a rebuild of a biocontainer with the latest version of a bioconda package?
18 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25465
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25467
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25477
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25479
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25482
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25487
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25489
Brent Pedersen
@brentp
Hi core, could I get a review on bioconda/bioconda-recipes#25435 ?
Brent Pedersen
@brentp
thanks @dpryan79
Devon Ryan
@dpryan79
:+1:
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25497
PR ready for review: bioconda/bioconda-recipes#25495
Bastian Schiffthaler
@bschiffthaler

Hi! I am currently adding bioconda/bioconda-recipes#25501 with variants for MPI (nompi, mpich and openmpi). Variants without MPI and MPICH build (and test) fine, but OpenMPI had issues testing:

Error:

10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR --------------------------------------------------------------------------
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR The value of the MCA parameter "plm_rsh_agent" was set to a path
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR that could not be found:
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR plm_rsh_agent: ssh : rsh
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR Please either unset the parameter, or check that the path is correct
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR --------------------------------------------------------------------------
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR [8c540ddec9fa:00012] [[INVALID],INVALID] FORCE-TERMINATE AT Not found:-13 - error plm_rsh_component.c(335)
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR [8c540ddec9fa:00010] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 716
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR [8c540ddec9fa:00010] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 172
10:08:36 BIOCONDA INFO (ERR) [Nov 24 10:08:36] SERR --------------------------------------------------------------------------

I'm not sure if this is on my end, but it looks like it may not be. Could it be a config issue in the build environment?

1 reply
M Bernt
@bernt-matthias
I'm just looking at a recipe where the github URL to the source archive does not exist anymore (maybe the tag/release has been removed?). Is there a workaround for such a case? : https://github.com/compomics/meta-proteome-analyzer/tags I'm looking for 1.4.1
Devon Ryan
@dpryan79
You might get lucky and find it archived on the galaxy cargo-port. That stores at least some source packages for bioconda. @bgruening would know more.
M Bernt
@bernt-matthias
Unfortunately its not there
OK. Thanks. Then we need to solve it on Galaxy side.
Gabriel Renaud
@grenaud
Hello! I get "test macos blocked", is there any way we can skip macos testing?
11 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25508
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25511
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25526
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25529
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25530
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25535
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25536
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25523
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25531
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25544
Kim
@kpj
Hey all, I added a new recipe (bioconda/bioconda-recipes#25504) which is ready for a review!
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25504
DrYak
@DrYak
Hi guys! My colleague @kpj has made PR bioconda/bioconda-recipes#25504,
I normally should have the necessary rights to do the review (and the PR looks good to me), but I wanted to ask I somebody could check if we're not missing something (I haven't kept up if there are changes in the recommendations).
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25500
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25547
Andrea Telatin
@telatin
Hello, what's the recommendation for Python version requirement?
I recommended putting the required version here, and the developer noted that it was forcing Python 3.8 installation
https://github.com/bioconda/bioconda-recipes/pull/25547#issuecomment-734431562 Is there a better way to recommend >3.4 for example?
Chen Ying
@cying111
Hello, I've just made a PR: bioconda/bioconda-recipes#25558 , could someone help to review? Thanks!
1 reply
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25553
Devon Ryan
@dpryan79
@telatin The way it's done in that PR is the recommended way. I kind of assume that miniconda2 (that should really be removed) can create python 3 envs, since miniconda3 can create python 2 envs.
M Bernt
@bernt-matthias
Could someone be so nice and check if the 2 recipes modified in bioconda/bioconda-recipes#25508 (encyclopedia and mpa-portable) made it to biocontainers. As far as I can see this seems not to be the case https://biocontainers.pro/#/tools/encyclopedia
If there was some problem, how do we get those containers updated?
Devon Ryan
@dpryan79
The biocontainers website doesn't seem to get updated very often
M Bernt
@bernt-matthias
I accidentally merged a PR by clicking the merge button (so no @BiocondaBot please merge). Is this a problem?
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25562
Devon Ryan
@dpryan79
@bernt-matthias nah, not an issue, just uses some extra CI resources
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25572