star: init at 2.5.3a #34156

arcadio · 2018-01-22T18:31:31Z

Motivation for this change

Add star derivation.

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-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 nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Fits CONTRIBUTING.md.

dotlambda · 2018-01-22T22:50:24Z

pkgs/applications/science/biology/star/default.nix

+
+  buildPhase = ''
+    cd source
+    sed 's/\/bin\/rm/rm/g' Makefile > Makefile2


This should go into postPatch.

Use another separator to avoid escaping slashes. Also, use inline sed processing to avoid extra mv.

sed 's:/bin/rm:rm/g' -i Makefile

dotlambda · 2018-01-22T22:51:29Z

pkgs/applications/science/biology/star/default.nix

+  buildInputs = [ zlib ];
+
+  buildPhase = ''
+    cd source


Why not use sourceRoot? See https://nixos.org/nixpkgs/manual/#ssec-unpack-phase.

Sure, what's the idiomatic way to do this? sourceRoot = "source/source";?

Just sourceRoot = "source" should be fine.

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 ]; }; }

Looks alright 👍

rasendubi · 2018-01-22T23:50:54Z

pkgs/applications/science/biology/star/default.nix

+{ stdenv, fetchFromGitHub, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "star";


Include version into the name attribute. Nix parses package version from name attribute and version one has no special meaning.

rasendubi · 2018-01-22T23:52:41Z

pkgs/applications/science/biology/star/default.nix

+
+  buildPhase = ''
+    cd source
+    sed 's/\/bin\/rm/rm/g' Makefile > Makefile2


Use another separator to avoid escaping slashes. Also, use inline sed processing to avoid extra mv.

sed 's:/bin/rm:rm/g' -i Makefile

rasendubi · 2018-01-22T23:55:07Z

pkgs/applications/science/biology/star/default.nix

+  meta = with stdenv.lib; {
+    description = "Spliced Transcripts Alignment to a Reference";
+    homepage = https://github.com/alexdobin/STAR;
+    license = licenses.gpl3;


It should be gpl3Plus.

rasendubi · 2018-01-22T23:56:29Z

pkgs/top-level/all-packages.nix

@@ -18962,6 +18962,8 @@ with pkgs;

  snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };

+  star = callPackage ../applications/science/biology/star/default.nix { };


default.nix is default path when calling a directory—do not specify it explicitly.

star = callPackage ../applications/science/biology/star { };

Done. Some packages in all-packages do explicitly specify this. I will try to clean them up, at least for the science section sometime.

rasendubi · 2018-01-23T15:38:26Z

lib/maintainers.nix

@@ -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>";


Do you mind naming the attribute after your GitHub username arcadio?

No, it's fine.

arcadio · 2018-01-23T18:51:19Z

All proposed changes done. Shall I squash into one commit?

rasendubi · 2018-01-24T15:08:05Z

Yes, squash, please.

arcadio · 2018-01-24T16:10:02Z

@rasendubi Squashed now.

disassembler · 2018-01-25T02:13:26Z

@GrahamcOfBorg build star

GrahamcOfBorg

Success for system: x86_64-linux

/nix/store/gzx9dy9zd867vm40h7pk9rg7zr70sgvc-star-2.5.3a

GrahamcOfBorg

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.

GrahamcOfBorg

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

GrahamcOfBorg added 10.rebuild-darwin: 0 10.rebuild-linux: 1-10 labels Jan 22, 2018

dotlambda reviewed Jan 22, 2018

View reviewed changes

rasendubi reviewed Jan 22, 2018

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rasendubi reviewed Jan 23, 2018

View reviewed changes

star: init at 2.5.3a

72d675b

GrahamcOfBorg reviewed Jan 25, 2018

View reviewed changes

rasendubi merged commit 38fbc93 into NixOS:master Jan 27, 2018

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star: init at 2.5.3a #34156

star: init at 2.5.3a #34156

arcadio commented Jan 22, 2018 •

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arcadio commented Jan 23, 2018

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arcadio commented Jan 24, 2018

disassembler commented Jan 25, 2018

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		@@ -18962,6 +18962,8 @@ with pkgs;

		snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };

		star = callPackage ../applications/science/biology/star/default.nix { };

star: init at 2.5.3a #34156

star: init at 2.5.3a #34156

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arcadio commented Jan 22, 2018 • edited Loading

Motivation for this change

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arcadio commented Jan 23, 2018

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arcadio commented Jan 22, 2018 •

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