Add Gapseq #47417

cmkobel · 2024-04-23T17:23:45Z

Add gapseq

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cmkobel · 2024-04-24T12:17:13Z

@BiocondaBot please add label

cmkobel · 2024-04-24T12:29:24Z

In response to jotech/gapseq#60

cmkobel · 2024-04-29T06:45:55Z

Awaiting review.

bgruening · 2024-04-30T11:34:21Z

recipes/gapseq/build.sh

+
+# Install one additional R-package
+# CHNOSZ is now available on bioconda and is already part of the dependencies.
+# R -e 'install.packages("CHNOSZ", repos="http://cran.us.r-project.org")' 


We should not install R packages this way.
I guess we need to go the extra round and create those packages in conda-forge. https://conda-forge.org/docs/maintainer/adding_pkgs/#generating-the-recipe

I can help you reviewing them over at conda-forge if you ping me.

Hi bgruening. Thanks for reviewing the recipe.
This is just a comment from the "conda" installation instructions of the gapseq package that I'm basing this recipe off of. The package is installed through conda r::chnosz.

Yes, see below, we need everything in conda-forge or bioconda.

I submitted a recipe to conda-forge using your skeleton helper.
conda-forge/staged-recipes#26190

I believe that it is ready for merging.

bgruening · 2024-04-30T11:35:06Z

recipes/gapseq/meta.yaml

+
+requirements:
+  run:
+    - r-base =4.3 # Version specification is not strictly necessary, but can help avoiding future sudden problems due to incompatible changes to R.


please remove the pin, we pin those packages during the build so its not needed here.

bgruening · 2024-04-30T11:35:40Z

recipes/gapseq/meta.yaml

+    - r-glpkapi
+    - r-rcurl
+    - r-httr
+    - r::r-chnosz # Is available on bioconda directly


is or is not?

If it is only available in this channel please create a package in conda-forge for this one. Thanks

Sorry, I'm confusing the channels. It is only on R. will update.

Should I copy the recipe from r to conda-forge?

bgruening · 2024-04-30T11:35:53Z

recipes/gapseq/meta.yaml

+  home: https://github.com/jotech/gapseq
+  summary: Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks 
+  license_family: GPL
+  license: GPL-3.0


please use the SPDX identifier

bgruening · 2024-04-30T11:36:14Z

recipes/gapseq/meta.yaml

+  license_file: LICENSE
+extra:
+  skip-lints:
+    - should_be_noarch_generic


why is it not noarch: generic?

Because the linter gives this error, even though it is not noarch_generic (doesn't work on macos).

cmkobel · 2024-05-03T20:06:55Z

@bgruening now when r-chosz is added to conda-forge, we can add gapseq to bioconda. What do you think?

cmkobel · 2024-05-07T11:05:31Z

@BiocondaBot please add label

recipes/gapseq/meta.yaml

Co-authored-by: Björn Grüning <[email protected]>

cmkobel · 2024-05-12T13:28:02Z

@bgruening does everything look good to you?

bgruening

@cmkobel thanks!

* init * passes bioconda-utils lint * works too * polishing * final test * ensure correct pinning * minor tweaks * test was too long. * amend * work on tests after package has been published * updates according to bgruening's comments * r-chnosz is now available on conda-forge * amend * reset build number * Update recipes/gapseq/meta.yaml Co-authored-by: Björn Grüning <[email protected]> --------- Co-authored-by: Björn Grüning <[email protected]>

cmkobel · 2024-05-14T07:21:43Z

The linter for the push of this merge yields

"No hosted parallelism has been purchased or granted. To request a free parallelism grant, please fill out the following form https://aka.ms/azpipelines-parallelism-request".

What can I do?

martin-g · 2024-05-14T07:31:47Z

What can I do?

Just wait.
See #41025 (comment)

cmkobel · 2024-05-23T15:55:10Z

Hi, I read that the parallelism issue was fixed which is great.

But, it seems like the old merge (6031d1a) by @daler hasn't been rerun and still is stuck as failed on the CI test.

Can I do something to have the merge CI re-run?

Best, Carl

cmkobel · 2024-05-24T09:36:36Z

There are still no signs of gapseq becoming available on bioconda.
Should I revert the merge and we can try again? @bgruening?

Best, Carl

aliciaaevans · 2024-05-24T13:07:48Z

The nightly uploader picked it up and it built successfully. Looks like it's in the channel: https://anaconda.org/bioconda/gapseq

There is sometimes a lag between when it's uploaded and when it's available from the CDN. Can you please try again? I am able to install it.

cmkobel · 2024-05-24T13:39:38Z

Thanks!! Great.

cmkobel added 6 commits April 23, 2024 16:53

init

c2fde19

passes bioconda-utils lint

5fde5e3

works too

6ce29f5

polishing

4af805b

final test

27a8ba0

ensure correct pinning

1172052

BiocondaBot added the please review & merge set to ask for merge label Apr 24, 2024

cmkobel added 5 commits April 26, 2024 09:39

minor tweaks

675aedd

Merge branch 'master' into gapseq

fa6ec10

test was too long.

a665327

amend

5a72846

work on tests after package has been published

914ba7e

bgruening reviewed Apr 30, 2024

View reviewed changes

updates according to bgruening's comments

6fe72b3

cmkobel mentioned this pull request May 3, 2024

Add r-chnosz conda-forge/staged-recipes#26190

Merged

10 tasks

cmkobel added 3 commits May 3, 2024 13:27

r-chnosz is now available on conda-forge

7113d80

amend

b8c8bba

reset build number

2fa38ca

bgruening reviewed May 8, 2024

View reviewed changes

recipes/gapseq/meta.yaml Outdated Show resolved Hide resolved

cmkobel and others added 2 commits May 8, 2024 12:22

Update recipes/gapseq/meta.yaml

5cc1933

Co-authored-by: Björn Grüning <[email protected]>

Merge branch 'master' into gapseq

c411e3d

bgruening approved these changes May 12, 2024

View reviewed changes

bgruening merged commit 957c6af into bioconda:master May 12, 2024
6 checks passed

cmkobel mentioned this pull request May 24, 2024

Add gapseq to bioconda jotech/gapseq#217

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Add Gapseq #47417

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Add Gapseq #47417

Add Gapseq #47417

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cmkobel commented Apr 23, 2024

General instructions

Instructions for avoiding API, ABI, and CLI breakage issues

Bot commands for PR management

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