Add biom-format - Githubissues

biocore / conda-recipes

conda recipes for bioinformatic tools like blast+, infernal, etc.

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Add biom-format #36

Closed colinbrislawn closed 8 years ago

colinbrislawn commented 8 years ago

I know this would be covered in #3, but biom-format is a stand-alone project, it is being updated as part of QIIME 2, and I would find it immediately useful.

wasade commented 8 years ago

:+1:, ideally this ensures h5py comes with it On Nov 10, 2015 09:02, "Colin Brislawn" notifications@github.com wrote:

https://github.com/biocore/biom-format

I know this would be covered in #3 https://github.com/biocore/conda-recipes/issues/3, but biom-format is a stand-alone project, it is being updated as part of QIIME 2, and I would find it immediately useful.

— Reply to this email directly or view it on GitHub https://github.com/biocore/conda-recipes/issues/36.

colinbrislawn commented 8 years ago

Exactly! And biom from-uc.

conda config --add channels http://conda.anaconda.org/biocore
conda install vsearch biom

:flushed:

gregcaporaso commented 8 years ago

I have a couple of updates (#645 and #679) going into biom this week which I think would be generally useful. If you could hold off for a few days on this one, I could probably get a 2.1.6 up that has these new pieces.

colinbrislawn commented 8 years ago

I've been working on this one, but some more experienced should take it. (I've been recreating the .travis.yml of biom-format as a conda-recipe. Very slow going...)

Jorge-C commented 8 years ago

Hi Colin, just a couple of tips that might help you. Sorry if you're already familiar with them!

biom-format is pip installable, so you can use conda skeleton to create an initial recipe.
It might be missing h5py/numpy as dependencies, so you might have to play with that

Let us know if you're stuck in a specific problem!

colinbrislawn commented 8 years ago

Oh, I did not know this was on pip. Duh. Thank you! I'll take another shot.

Colin

On Mon, Nov 16, 2015, 11:52 AM Jorge Cañardo Alastuey < notifications@github.com> wrote:

Hi Colin, just a couple of tips that might help you. Sorry if you're already familiar with them!

biom-format is pip installable, so you can use conda skeleton http://conda.pydata.org/docs/commands/build/conda-skeleton.html to create an initial recipe.

It might be missing h5py/numpy as dependencies, so you might have to play with that

Let us know if you're stuck in a specific problem!

— Reply to this email directly or view it on GitHub https://github.com/biocore/conda-recipes/issues/36#issuecomment-157150185 .

colinbrislawn commented 8 years ago

Thanks to @bgruening, biom-format is now on bioconda. We will troubleshoot any h5py issues there. https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biom-format

wasade commented 8 years ago

That is fantastic, thank you @bgruening!

On Mon, Mar 7, 2016 at 9:28 AM, Colin Brislawn notifications@github.com wrote:

Closed #36 https://github.com/biocore/conda-recipes/issues/36.

— Reply to this email directly or view it on GitHub https://github.com/biocore/conda-recipes/issues/36#event-580472215.