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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
Arun Patil
@arunhpatil
Hi, please review this. bioconda/bioconda-recipes#25570
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25576
sureshhewa
@sureshhewabi
Hi, I am new to bioconda. I updated my recipe with this PR: https://github.com/bioconda/bioconda-recipes/pull/25576/ How long it takes to update anaconda? I am expecting build no 1 here. But Still it should 0. Any comments?
Nicola Soranzo
@nsoranzo
It takes some hours
Devon Ryan
@dpryan79
I forgot to merge that, sorry about that. Give it maybe 30 minutes after the bot merges it in to be available.
sureshhewa
@sureshhewabi
Thanks all
this is my tool. I created an wrapper "submission-tool-validator.py " to call that jar.
I created an conda environment: conda create --name submission-tool-validator-new -c bioconda submission-tool-validator
how can I ran the tool now?
I tried "python3 submission-tool-validator.py" and it didn't work
1 reply
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#24295
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25582
RNieuwenhuis
@RNieuwenhuis
Hi, if it comes to writing recipes I am quite a novice. Is use of git_url completely prohibited? In the guidelines it is stated as "Ideally". bioconda/bioconda-recipes#25584
2 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25593
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25588
Ralf Weber
@RJMW
I am adding a python package to bioconda that has matplotlib==3.1.3 and pyside2 as requirements.
I am getting the following error at the linting stage: ERROR: recipes/metabolabpy/meta.yaml:0: uses_matplotlib: The recipe uses `matplotlib`, but `matplotlib-base` is recommended
What is the recommendation?
Nicola Soranzo
@nsoranzo
Replace matplotlib with matplotlib-base in the requirements
Ralf Weber
@RJMW
but pyside2 does need qt?
Devon Ryan
@dpryan79
@RJMW you can add a skip lint and keep matplotlib. https://bioconda.github.io/contributor/linting.html#skipping-a-lint-check
If you need qt then the best approach
Xia Liu
@xialiu71
Hi, could I please get a review for my PR? I've tried pinging BiocondaBot but haven't gotten a label so I figured I'd ask here bioconda/bioconda-recipes#25598
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25598
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25598
Antônio Pedro Camargo
@apcamargo
I'm writing recipes for two python packages that use scripts in their setup.py. How should I "translate" this into a conda recipe?
I tried copying the script files into $PREFIX/bin, but it didn't work
Devon Ryan
@dpryan79
Those should be handled by pip
Yeah, pip will put those in $PREFIX/bin for you
Antônio Pedro Camargo
@apcamargo
so I don't need to do anything?
thanks!
Devon Ryan
@dpryan79
Exactly :)
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#25607
Antônio Pedro Camargo
@apcamargo
another quick question
I'm developing a software and I always do so with Bioconda in mind
but for this particular project I need a dependency that I can't put in conda-forge, even though the compiled library is in PyPI
Devon Ryan
@dpryan79
@apcamargo Why can't it go in conda-forge or bioconda?
Antônio Pedro Camargo
@apcamargo
The source isn't in PyPI, just GitHub
PyPI has the compiled build