diamond: init at 0.8.36 #23111
diamond: init at 0.8.36 #23111
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Any comment (in the package source) why the patch is necessary would be nice. Also: If this patch is needed to be able to compile the package, consider contributing this patch upstream! |
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The patch is just to remove two warnings during the compilation. I can send it to the authors but in the meantime where and how should I explain the patch ? in the default.nix file ? |
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| patches = [ | ||
| ./diamond-0.8.36.patch | ||
| ]; |
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| sourceRoot = "diamond-0.8.36"; | ||
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| buildInputs = [ cmake gcc zlib ]; |
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gcc should not be necessary. cmake should be in nativeBuildInputs.
| DNA-protein search on short reads and longer sequences including contigs | ||
| and assemblies, providing a speedup of BLAST ranging up to x20,000. | ||
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| DIAMOND is developed by Benjamin Buchfink. Feel free to contact him for support (Email Twitter). |
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Indent whole longDescription two spaces right.
| If you use DIAMOND in published research, please cite | ||
| B. Buchfink, Xie C., D. Huson, | ||
| "Fast and sensitive protein alignment using DIAMOND", | ||
| Nature Methods 12, 59-60 (2015). |
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Indent this paragraph 6 spaces right.
| homepage = https://github.com/bbuchfink/diamond; | ||
| license = { | ||
| fullName = "University of Tuebingen, Benjamin Buchfink"; | ||
| url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING; |
| license = { | ||
| fullName = "University of Tuebingen, Benjamin Buchfink"; | ||
| url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING; | ||
| }; |
| } | ||
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Please remove the empty lines here.
| ./diamond-0.8.36.patch | ||
| ]; | ||
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| sourceRoot = "diamond-0.8.36"; |
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Are you sure this is necessary? This should be detected automatically.
| }; | ||
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| patches = [ | ||
| ./diamond-0.8.36.patch |
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You could give the patch a more telling name like fix-warnings.patch.
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Thank you for your comments. With the commit 20fd13d86caa4be6b872283d7038a3c2f7df05f3, I hope that I have fulfill all the requests from the previous review. |
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I had some problems because of a synchronization between the NixOS:master and of metabarcoding:master. I tried to isolate the diamond package in a single commit by merging the different branches on our side before recreating the files and commit them in a single commit : 20fd13d86caa4be6b872283d7038a3c2f7df05f3. Now I don't know how to "It should be cleaned up first!" |
what is that for a repository and why do you need it? And why do you need to stay up to date with nixos master branch for a new package? |
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Ok, it did a mistake, perhaps I didn't say it enough clearly. But now that the mistake exists how can I clean things to be in the right way ? Perhaps can I clear the metabarcoding:diamond branch, create a new one and ask for a new Pull request, this should clean up the extra commits Thank you for your help. |
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So it seems that your branch is based on 9ae8ce8. I guess you can Then, you can push this branch again... |
into diamond Conflicts: pkgs/applications/science/biology/diamond/default.nix
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was merged in #24840 |
Motivation for this change
This is a new package, DIAMOND, a bioinformatics tool to perform that implements an accelerated BLAST compatible local sequence aligner.
B. Buchfink, Xie C., D. Huson, Fast and sensitive protein alignment using DIAMOND, Nature Methods 12, 59-60 (2015).
Things done
(nix.useSandbox on NixOS,
or option
build-use-sandboxinnix.confon non-NixOS)
nix-shell -p nox --run "nox-review wip"./result/bin/)