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GenEra Conda Recipes Submission #51721

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GenEra Conda Recipes Submission #51721

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Committer: Anupam Gautam <[email protected]>
Oct 24, 2024
6fdfb3b
Merge branch 'bioconda:master' into update_my_recipe
AnupamGautam Oct 25, 2024
4ab01ae
Update recipes/tipp/build.sh
AnupamGautam Oct 25, 2024
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Update recipes/tipp/build.sh
AnupamGautam Oct 25, 2024
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Update recipes/tipp/build.sh
AnupamGautam Oct 25, 2024
61cdfda
Update recipes/tipp/build.sh
AnupamGautam Oct 25, 2024
9ed0cdd
Update recipes/tipp/build.sh
AnupamGautam Oct 25, 2024
2c0a077
Update recipes/tipp/meta.yaml
AnupamGautam Oct 25, 2024
c9d79ab
Merge branch 'bioconda:master' into update_my_recipe
AnupamGautam Oct 25, 2024
01a006d
Committer: Anupam Gautam <[email protected]>
Oct 25, 2024
c93d20d
Merge branch 'bioconda:master' into update_my_recipe
AnupamGautam Oct 25, 2024
8f24e82
Merge branch 'master' into update_my_recipe
AnupamGautam Oct 25, 2024
726f73b
Committer: Anupam Gautam <[email protected]>
Oct 25, 2024
6ca983f
Merge branch 'master' into update_my_recipe
AnupamGautam Oct 25, 2024
4fea052
Merge branch 'bioconda:master' into update_my_recipe
AnupamGautam Oct 28, 2024
455eaf3
GenEra conda recipes
Oct 28, 2024
7d21180
removed genera files
Oct 28, 2024
2e331f5
GenEra conda recipe
Oct 28, 2024
1c55c53
cleaning
Oct 28, 2024
8554955
Merge branch 'master' into update_my_recipe2
AnupamGautam Oct 28, 2024
7a4152e
Merge branch 'master' into update_my_recipe2
AnupamGautam Oct 28, 2024
103ce91
Merge branch 'bioconda:master' into update_my_recipe2
AnupamGautam Oct 28, 2024
579c149
update
Oct 28, 2024
759c679
Merge branch 'master' into update_my_recipe2
aliciaaevans Oct 29, 2024
5569775
Merge branch 'bioconda:master' into update_my_recipe2
AnupamGautam Oct 29, 2024
0305a7c
python updated
Oct 29, 2024
81192f3
changes added
Nov 1, 2024
448443e
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 1, 2024
88db21b
added test and abSENSE release
Nov 4, 2024
13ba689
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 4, 2024
449f892
added test and abSENSE release
Nov 4, 2024
bea8361
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 5, 2024
cb2bf56
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 7, 2024
463df26
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 11, 2024
7e87ce3
update
Nov 15, 2024
131d9d3
Merge branch 'master' into update_my_recipe2
richard-burhans Nov 15, 2024
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Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 16, 2024
43ab6b9
update
Nov 16, 2024
0203536
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 16, 2024
c34e66e
Update recipes/genera/meta.yaml
AnupamGautam Nov 18, 2024
50c9c61
Update recipes/genera/meta.yaml
AnupamGautam Nov 18, 2024
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Update meta.yaml
AnupamGautam Nov 18, 2024
f183729
Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 18, 2024
f4babdd
Solved abSENSE License issue
AnupamGautam Nov 18, 2024
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Merge branch 'master' into update_my_recipe2
AnupamGautam Nov 18, 2024
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30 changes: 30 additions & 0 deletions recipes/genera/build.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash

# Exit on any error
set -ex

# Ensure all main scripts are executable
chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh
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#Move the main Run_abSENSE.py script

mv abSENSE/Run_abSENSE.py .
chmod +x Run_abSENSE.py

# Define the Conda binary path
CONDABIN="${PREFIX}/bin"

# Ensure the directory exists
mkdir -p "$CONDABIN"


# Move executables to the Conda binary directory
mv genEra "$CONDABIN"
mv Erassignment "$CONDABIN"
mv Run_abSENSE.py "$CONDABIN"
mv hmmEra "$CONDABIN"
mv tree2ncbitax "$CONDABIN"
mv FASTSTEP3R "$CONDABIN"
mv test_installation.sh "$CONDABIN"

echo "Installation complete. Executables have been moved to ${CONDABIN}."
42 changes: 42 additions & 0 deletions recipes/genera/meta.yaml
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package:
name: genera
version: "1.4.2"

source:
- url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz
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sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54
- url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.0.tar.gz
sha256: a99090c10a66afae1fbad38d79d228199e9fbdae5173e71ad5d84b4c958dda54
folder: abSENSE
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Is there a reason this is not a separate recipe?

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@AnupamGautam AnupamGautam Nov 18, 2024 •
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Dear @mfansler,

I have implemented your suggestions and added a new test as well. Regarding the tool abSENSE, I have reached out to the author to confirm their interest in having a Conda package. If they express interest, I can create a PR for the package.

For now, we can proceed like this, and if author want I can create a PR later ,and update this package also. Could you please approve the workflow so that it can start? Thank you so much for your help!

Best regards,
Anupam

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As far as I see, abSENSE has no licensing declared, which is prohibitive to bundling it for Bioconda. Please ask the author to declare a license and include that in a release.

Once there is a license it should be moved to a separate package here. Note that the author does not have to be a maintainer here.

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Dear @mfansler,

I had reached out to the authors a few weeks ago regarding the LICENSE, release, and a potential Conda package. Since then, they have created a release for us, but I assume a Conda package may not be something they are prioritizing.

This code is part of a published open-access paper, and I believe it is included in the supplementary materials. In this case, would a license still be required for the Conda package?

Here’s the relevant issue for reference: abSENSE Issue #3.

Here's the paper: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000862

They also mention in paper:"An implementation of our method, with all raw data and results presented here, is freely available as source code at github.com/caraweisman/abSENSE and as a web server at eddylab.org/abSENSE."
Thank you for your guidance!

Best regards,
Anupam

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Thanks for the additional information!

While the article itself is CC-BY-4.0, a copy of the code does not appear deposited with the article and thus it is not covered. If they want to extend exactly the same license, they could put a copy of the CC-BY-4.0 text in the repository somewhere.

Otherwise, unfortunately "open-source" doesn't translate to permission to redistribute.

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Hi @mfansler,

I have reached out to the author again for clarification. Once they respond, I will proceed as suggested. However, if they decide against having a Conda package but provide a license, I can move forward using the current approach?

Thank you for your support!

Additionally, could you please help me start the workflow for my other recipe? It doesn’t seem to start automatically. Your assistance would be greatly appreciated.: TIPP_plastid conda recipe.

Best regards,
Anupam

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@AnupamGautam AnupamGautam Nov 18, 2024 •
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Dear @mfansler,

The authors have added a license file to their repository and released a new version. I’ve updated the meta.yaml file to include this latest release. While they may still need time to decide whether they want an official Conda package, I can create one for them later if requested and make the necessary updates.

For now, we can proceed with the current setup. Could you help initiate the workflow and assist in merging this?

Thank you for your continued support!

Best regards,
Anupam


build:
number: 0
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This package should be noarch generic I think

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Added.

run_exports:
- {{ pin_subpackage('genera', max_pin="x.x") }}
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🛠️ Refactor suggestion

Remove unnecessary run_exports section.

Since this is a noarch: generic package, the run_exports section with pin_subpackage is unnecessary and could lead to overly strict version constraints.

 build:
   number: 0
   noarch: generic
-  run_exports:
-    - {{ pin_subpackage('genera', max_pin="x.x") }}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
run_exports:
- {{ pin_subpackage('genera', max_pin="x.x") }}


requirements:
host:
- python =3.8.0
run:
- python =3.8.0
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please do not spin that strict, this is not how conda works. Strict pins can be used in environments.yml files, but packages should specify pins when they are really incompatible.

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Hi @bgruening, I’ve added a non-strict version specification for Python, but some other packages need specific version constraints as certain required flags are only available in those versions.

- diamond =2.1.10
- mmseqs2 =14.7e284
- foldseek =3.915ef7d
- scipy =1.7.3
- r-seqinr =4.2_16
- r-optparse =1.7.3
- r-bio3d =2.4_3
- r-tidyverse =1.3.2
- r-phytools =0.6_99
- orthofinder =2.5.5
- ncbitax2lin =2.3.2

test:
commands:
- genEra -h 2>&1 > /dev/null
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about:
home: https://github.com/josuebarrera/GenEra
license: "GPL-3.0"
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Please use SDPX identifiers

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added

license_family: GPL3
summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra"
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