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SPAdes: add python dependency #89778

Merged
merged 1 commit into from Dec 21, 2020
Merged

SPAdes: add python dependency #89778

merged 1 commit into from Dec 21, 2020

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jbedo
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@jbedo jbedo commented Jun 7, 2020

Motivation for this change

spades.py requires python.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@jbedo jbedo requested a review from bzizou June 7, 2020 23:42
jtojnar
jtojnar requested changes Jun 8, 2020
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The commit message tag needs to match the attribute name SPAdes.

pkgs/applications/science/biology/spades/default.nix Outdated Show resolved Hide resolved
@jbedo jbedo requested a review from jtojnar June 8, 2020 11:20
@jbedo jbedo changed the title spades: add python dependency SPAdes: add python dependency Jun 8, 2020
@SuperSandro2000
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Build in #87494 fine without. Closing.

@jbedo
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jbedo commented Nov 28, 2020 via email

@jbedo
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jbedo commented Nov 28, 2020 •
edited

@SuperSandro2000 Confirmed, patch still required:

~/g/nixpkgs on 8256fc2da56 ⨯ nix shell .#SPAdes -c spades.py
/usr/bin/env: ‘python’: No such file or directory

@jbedo jbedo reopened this Nov 28, 2020
@ofborg ofborg bot requested a review from bzizou November 28, 2020 08:46
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jbedo commented Dec 14, 2020

SPAdes is unusable without this patch, is there anything further I need to do to get it merged? Might be worth considering backporting to 20.09 since it's also broken there.

bzizou
bzizou approved these changes Dec 15, 2020
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I agree that the python dependency allows spades.py to run in a pure environment without explicitly loading python

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I read on their GitHub that they support python3 https://github.com/ablab/spades#installation. Can we please use python3 as we are currently remove python2 from as many packages as possible.

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jbedo commented Dec 20, 2020

Changed to python 3, rebased against current master, and verified functional.

@ofborg ofborg bot requested a review from bzizou December 20, 2020 21:45
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Result of nixpkgs-review pr 89778 run on x86_64-darwin 1

1 package built:
  • SPAdes

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Result of nixpkgs-review pr 89778 run on x86_64-linux 1

1 package built:
  • SPAdes

@SuperSandro2000 SuperSandro2000 merged commit af69f39 into NixOS:master Dec 21, 2020
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@bzizou bzizou bzizou approved these changes

@jtojnar jtojnar Awaiting requested review from jtojnar

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@jbedo @SuperSandro2000 @jtojnar @bzizou