PR ready for review: bioconda/bioconda-recipes#25495
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
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
OK. Thanks. Then we need to solve it on Galaxy side.
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).
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).
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?
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?
Hello, I've just made a PR: bioconda/bioconda-recipes#25558 , could someone help to review? Thanks!
1 reply
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?
The biocontainers website doesn't seem to get updated very often