star: init at 2.5.3a #34156
star: init at 2.5.3a #34156
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| buildPhase = '' | ||
| cd source | ||
| sed 's/\/bin\/rm/rm/g' Makefile > Makefile2 |
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This should go into postPatch.
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Use another separator to avoid escaping slashes. Also, use inline sed processing to avoid extra mv.
sed 's:/bin/rm:rm/g' -i Makefile| buildInputs = [ zlib ]; | ||
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| buildPhase = '' | ||
| cd source |
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Why not use sourceRoot? See https://nixos.org/nixpkgs/manual/#ssec-unpack-phase.
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Sure, what's the idiomatic way to do this? sourceRoot = "source/source";?
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Just sourceRoot = "source" should be fine.
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I had tried sourceRoot = "source" already, but it didn't work. I might be missing something entirely obvious as I'm migrating packages from Guix, and there are some subtle differences.
Note that STAR has a source directory, which shows up inside Nix-created source after unpacking. This is the derivation I'm using, which works fine:
{ stdenv, fetchFromGitHub, zlib }:
stdenv.mkDerivation rec {
name = "star-${version}";
version = "2.5.3a";
src = fetchFromGitHub {
repo = "STAR";
owner = "alexdobin";
rev = version;
sha256 = "1fd9xl7i1zxgsxn2qf6gz8s42g2djm29qmp6qb35d8nnxh8ns54x";
};
sourceRoot = "source/source";
postPatch = "sed 's:/bin/rm:rm:g' -i Makefile";
buildInputs = [ zlib ];
buildPhase = "make STAR STARlong";
installPhase = ''
mkdir -p $out/bin
cp STAR STARlong $out/bin
'';
meta = with stdenv.lib; {
description = "Spliced Transcripts Alignment to a Reference";
homepage = https://github.com/alexdobin/STAR;
license = licenses.gpl3Plus;
platforms = platforms.linux;
maintainers = [ maintainers.arc ];
};
}
| { stdenv, fetchFromGitHub, zlib }: | ||
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| stdenv.mkDerivation rec { | ||
| name = "star"; |
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Include version into the name attribute. Nix parses package version from name attribute and version one has no special meaning.
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| buildPhase = '' | ||
| cd source | ||
| sed 's/\/bin\/rm/rm/g' Makefile > Makefile2 |
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Use another separator to avoid escaping slashes. Also, use inline sed processing to avoid extra mv.
sed 's:/bin/rm:rm/g' -i Makefile| meta = with stdenv.lib; { | ||
| description = "Spliced Transcripts Alignment to a Reference"; | ||
| homepage = https://github.com/alexdobin/STAR; | ||
| license = licenses.gpl3; |
pkgs/top-level/all-packages.nix
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| @@ -18962,6 +18962,8 @@ with pkgs; | |||
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| snpeff = callPackage ../applications/science/biology/snpeff/default.nix { }; | |||
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| star = callPackage ../applications/science/biology/star/default.nix { }; | |||
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default.nix is default path when calling a directory—do not specify it explicitly.
star = callPackage ../applications/science/biology/star { };
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Done. Some packages in all-packages do explicitly specify this. I will try to clean them up, at least for the science section sometime.
lib/maintainers.nix
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| @@ -55,6 +55,7 @@ | |||
| antonxy = "Anton Schirg <anton.schirg@posteo.de>"; | |||
| apeschar = "Albert Peschar <albert@peschar.net>"; | |||
| apeyroux = "Alexandre Peyroux <alex@px.io>"; | |||
| arc = "Arcadio Rubio García <arc@well.ox.ac.uk>"; | |||
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Do you mind naming the attribute after your GitHub username arcadio?
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All proposed changes done. Shall I squash into one commit? |
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Yes, squash, please. |
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@rasendubi Squashed now. |
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@GrahamcOfBorg build star |
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Failure for system: x86_64-darwin
Package ‘star-2.5.3a’ in /Users/graham/nix-borg/repo/38dca4e3aa6bca43ea96d2fcc04e8229/builder/grahamc-zoidberg/pkgs/applications/science/biology/star/default.nix:28 is not supported on ‘x86_64-darwin’, refusing to evaluate.
a) For `nixos-rebuild` you can set
{ nixpkgs.config.allowBroken = true; }
in configuration.nix to override this.
b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
{ allowBroken = true; }
to ~/.config/nixpkgs/config.nix.
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Success for system: aarch64-linux
installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a
shrinking /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a/bin/STARlong
shrinking /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a/bin/STAR
strip is /nix/store/jwz859pxqj7sl2dbwvmxkx68jp774izb-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a/bin
patching script interpreter paths in /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a
checking for references to /build in /nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a...
/nix/store/37v00rrawwwvlpxi0x1nrk98zr1yansq-star-2.5.3a
Motivation for this change
Add star derivation.
Things done
build-use-sandboxinnix.confon non-NixOS)nix-shell -p nox --run "nox-review wip"./result/bin/)