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Merged
merged 2 commits into from
Jun 14, 2019
Merged

cd-hit: init at 4.8.1 #58362

merged 2 commits into from
Jun 14, 2019
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bzizou
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@bzizou bzizou commented Mar 26, 2019

Motivation for this change

Biology tool needed in our computing center (GRICAD)

Things done
  • [ X Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • 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 nix-review --run "nix-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)
  • Assured whether relevant documentation is up to date
  • Fits CONTRIBUTING.md.

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@GrahamcOfBorg GrahamcOfBorg added 8.has: package (new) This PR adds a new package 11.by: package-maintainer This PR was created by the maintainer of the package it changes 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Mar 26, 2019
@bzizou bzizou changed the title [cd-hit] init at 4.8.1 cd-hit: init at 4.8.1 Mar 26, 2019
aanderse
aanderse requested changes Apr 14, 2019
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In the $out/bin folder there are many perl files, most some of which fail to execute as they cannot find the perl modules they depend on.

  • plot_2d.pl requires Image::Magick
  • FET.pl requires Text::NSP::Measures::2D::Fisher::right and clstr_list.pl
  • clstr_list_sort.pl and clstr_list.pl require Storable

@aanderse aanderse added the 9.needs: reporter feedback This issue needs the person who filed it to respond label Apr 29, 2019
@bzizou
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bzizou commented Apr 29, 2019

I'll check the dependencies problem of the perl files, asap (end of this week I think). Many thanks for this suggestion

@globin
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globin commented May 18, 2019

ping @bzizou

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bzizou commented May 21, 2019

pong @globin , sorry, I had some personal contingencies, so a bit late with almost every lines of my TODO list ;-)

@bzizou bzizou force-pushed the cd-hit branch 2 times, most recently from 320c9fe to 4b1fec6 Compare May 23, 2019 10:00
aanderse
aanderse requested changes Jun 12, 2019
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@bzizou Sorry for the delay this sorta fell off my radar. Just need the perl package in a separate commit and I think we're good to go... Do you agree @jtojnar?

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@GrahamcOfBorg build perlPackages.TextNSP perldevelPackages.TextNSP cd-hit

@aanderse aanderse merged commit 4cb64db into NixOS:master Jun 14, 2019
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8.has: package (new) This PR adds a new package 9.needs: reporter feedback This issue needs the person who filed it to respond 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 11.by: package-maintainer This PR was created by the maintainer of the package it changes
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