a19cd4ffb1
This reverts commit 65a333600d5c88a98d674f637d092807cfc12253. This wasn't tested for correctness with something like fodwatch [0], and should not have been (self-)merged so quickly, especially without further review. It also resulted in the breakage of at least one package [1] (and that's the one we know of and was caught). A few packages that were updated in between this commit and this revert were not reverted back to using `rev`, but other than that, this is a 1:1 revert. [0]: https://codeberg.org/raphaelr/fodwatch [1]: https://github.com/NixOS/nixpkgs/pull/396904 / 758551e4587d75882aebc21a04bee960418f8ce9
135 lines
3.6 KiB
Nix
135 lines
3.6 KiB
Nix
# Instructions:http://www.ensembl.org/info/docs/api/api_installation.html,
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# Do not use https://github.com/Ensembl/ensembl-vep/archive/release/${version}.zip
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# We cannot use INSTALL.pl but it’s not that bad:install the dependencies and copies the .pm files should be ok
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{
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lib,
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htslib,
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perlPackages,
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stdenv,
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fetchFromGitHub,
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perl,
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makeWrapper,
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}:
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let
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version = "110";
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customInstallPhase = ''
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mkdir -p $out/${perl.libPrefix}/${perl.version}/
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tests=$(find modules/ -mindepth 1 -maxdepth 1 -type d | grep -v t)
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cp -r $tests $out/${perl.libPrefix}/${perl.version}/
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'';
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ensemblGit =
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name: sha256:
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# Copy modules directly
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stdenv.mkDerivation {
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inherit name version;
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src = fetchFromGitHub {
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inherit sha256 version;
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owner = "Ensembl";
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repo = name;
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rev = "release/${version}";
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};
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installPhase = ''
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runHook preInstall
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${customInstallPhase}
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runHook postInstall'';
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};
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vepPlugins = fetchFromGitHub {
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owner = "Ensembl";
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repo = "VEP_plugins";
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rev = "8f271c4848338dc7d504881ff71fdf2892c3d096";
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sha256 = "sha256-LbaXwLFDP3m1QhRHwO9uh36BEFHE2NzL4xdxTb7/S5Q=";
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};
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# Install ensembl-xs, faster run using re-implementation in C of some of the Perl subroutines
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ensembl-xs = perlPackages.buildPerlPackage rec {
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pname = "ensembl-xs";
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version = "2.3.2";
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src = fetchFromGitHub {
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inherit version;
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owner = "Ensembl";
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repo = "ensembl-xs";
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rev = version;
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sha256 = "1qqnski532f4bz32wxbqd9w1sz40rjh81ipp9p02k3rlaf1gp1fa";
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};
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# PREFIX is important
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configurePhase = ''
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perl Makefile.PL PREFIX=$out INSTALLDIRS=site
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'';
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# Test do not work -- wrong include path
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doCheck = false;
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};
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# it contains compiled versions of certain key subroutines used in VEP
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ensembl = ensemblGit "ensembl" "sha256-ZhI4VNxIY+53RX2uYRNlFeo/ydAmlwGx00WDXaxv6h4=";
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ensembl-io = ensemblGit "ensembl-io" "sha256-r3RvN5U2kcyghoKM0XuiBRe54t1U4FaZ0QEeYIFiG0w=";
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ensembl-variation = ensemblGit "ensembl-variation" "sha256-UjrLHF9EqI+Mp+SZR4sLNZUCGiA/UYhoFWtpwiKF8tM=";
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ensembl-funcgen = ensemblGit "ensembl-funcgen" "sha256-a9hxLBoXJsF5JWuRdpyOac1u033M8ivEjEQecuncghs=";
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in
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perlPackages.buildPerlModule rec {
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inherit version;
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pname = "vep";
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buildInputs =
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(with perlPackages; [
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ArchiveZip
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BioBigFile
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BioDBHTS
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BioExtAlign
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BioPerl
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DBI
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DBDmysql
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LWP
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JSON
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])
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++ [
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ensembl-xs
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ensembl
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ensembl-funcgen
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ensembl-io
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ensembl-variation
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];
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propagatedBuildInputs = [ htslib ];
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src = fetchFromGitHub {
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owner = "Ensembl";
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repo = "ensembl-${pname}";
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rev = "release/${version}";
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sha256 = "sha256-6lRdWV2ispl+mpBhkZez/d9PxOw1fkNUWeG8mUIqBJc=";
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};
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nativeBuildInputs = [ makeWrapper ];
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dontBuild = true;
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doCheck = false;
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outputs = [ "out" ];
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin
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install -D -m755 filter_vep vep $out/bin/
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wrapProgram $out/bin/vep \
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--prefix PERL5LIB : $out/${perl.libPrefix}/${perl.version}/ \
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--add-flags "--dir_plugins ${vepPlugins}"
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wrapProgram $out/bin/filter_vep \
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--prefix PERL5LIB : $out/${perl.libPrefix}/${perl.version}/
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${customInstallPhase}
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runHook postInstall
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'';
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meta = {
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homepage = "https://www.ensembl.org/info/docs/tools/vep/index.html";
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description = "Annotate genetics variants based on genes, transcripts, and protein sequence, as well as regulatory regions";
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license = lib.licenses.asl20;
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mainProgram = "vep";
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maintainers = with lib.maintainers; [ apraga ];
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platforms = lib.platforms.unix;
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};
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}
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