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  • Jan 26 23:36
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Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19829
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19837
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19841
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19856
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19864
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19470
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19876
emmannaemeka
@emmannaemeka
Running conda update tbl2asn does not update to the current tbl2asn
Devon Ryan
@dpryan79
Was the update merged in?
emmannaemeka
@emmannaemeka
I don't think so, but after running conda update tbl2asn i still get this error [NULL_Caption] This copy of tbl2asn is more than a year old. Please download the current version.
[tbl2asn 25.7]
Devon Ryan
@dpryan79
NCBI only supplies precompiled binaries and last I looked they didn't work on all systems. Until that's resolved we can't distribute them (they won't even work on our test infrastructure).
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19885
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19891
jpfeuffer
@jpfeuffer
Hi! Are there any packages in bioconda that require OpenGL? I am looking for some hints on how to handle such a dependency.
I've read about CDT packages for building and requiring the library to be present on the install host but I did not find any official documentation.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19803
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19803
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19896
Natasha Pavlovikj
@npavlovikj
@jpfeuffer , for OpenGL packages you will need to use the extended container image, https://bioconda.github.io/contributor/troubleshooting.html#using-the-extended-image. If that doesn't work, then you can add the CDT dependencies in the build section, e.g. https://github.com/bioconda/bioconda-recipes/blob/fb33b5f0572e44f10ef2d4e27955a22e5b45b6ce/recipes/bandage/meta.yaml.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19898
pvanheus
@pvanheus
so one workaround for the tbl2asn issue that is bedevilling prokka amongst other things is to fake the current time using faketime. I have a PR open to add libfaketime to conda-forge (conda-forge/staged-recipes#10664) - do people think this is an acceptible workaround?
jpfeuffer
@jpfeuffer
@npavlovikj Thank you very much I will give it a try!!
Devon Ryan
@dpryan79
@pvanheus Will it still produce correct results? I would have thought that the reason they program the binaries with an end date is because it won't generate the correct output afterward.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19900
pvanheus
@pvanheus
@dpryan79 I will check but as I understand it, yes. here is an implementation of a wrapper using Docker by Austin Davis-Richardson - the difference in my proposal is using conda not Docker.
Rens Holmer
@holmrenser
I am trying to update my genenotebook to nodejs version >12.14.0, which requires libstdc++ >= 6.0.20 (GLIBCXX_3.4.20). Apparently the available libstdc++ only goes to GLIBCXX_3.4.13. Any suggestions for a workaround? Have been googling for a day and not found anything helpful.
Devon Ryan
@dpryan79
@holmrenser That normally only happens when you distribute something precompiled. The nodejs on conda-forge appears to be built against the same libstdc++ version that we use in bioconda.
Rens Holmer
@holmrenser
That seems related indeed, I am building a meteor.js app, which ships its own nodejs. Looking into whether this can be overridden.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19912
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19917
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19914
PR ready for review: bioconda/bioconda-recipes#19923
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19926
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19910
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19936
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19941
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19944
Maarten-vd-Sande
@Maarten-vd-Sande
Can someone explain why pysam is not available in python3.8? The meta.yaml doesn't seem to specify a max python number, and as far as I understand none of its dependencies make use of python, so they shouldn't be blocking it. Their newest release 0.15.4 should be python3.8-friendly. What am I missing? :expressionless:
Devon Ryan
@dpryan79
Nothing is built for python 3.8 since conda-forge hasn't finished its migration yet
Maarten-vd-Sande
@Maarten-vd-Sande
What's involved in the migration? Python3.8 is currently available on conda-forge. I'm trying to understand the mechanism
Devon Ryan
@dpryan79
Many conda-forge packages have been migrated, they're nearing the end. See https://conda-forge.org/status/
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19965
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19794
Maarten-vd-Sande
@Maarten-vd-Sande
Okay, thanks for the explanation and link @dpryan79 :smile:
pvanheus
@pvanheus
Hi bioconda people... so I got libfaketime into conda-forge which lets me fake the current time and make tbl2asn work - the only place to get an old tbl2asn binary, though, is by unpacking a bioconda package, as implemented e.g. here: https://github.com/audy/tbl2asn-forever/blob/master/Dockerfile
I could bump the build number and build a new bioconda recipe around this but that is rather a hack - what do people think? the other alternative is to not touch the existing message and patch users of this took (such as prokka).
Devon Ryan
@dpryan79
I would suggest trying to contact NCBI instead.
pvanheus
@pvanheus
hah. yes everyone is doing that too. no luck so far
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19977
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#19978