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dependencies.nix
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dependencies.nix
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with import ./nixpkgs;
let
# from nixpkgs/pkgs/applications/networking/cluster/mesos/default.nix
tarWithGzip = lib.overrideDerivation gnutar (oldAttrs: {
builder = "${bash}/bin/bash";
buildInputs = (oldAttrs.buildInputs or []) ++ [ makeWrapper ];
postInstall = (oldAttrs.postInstall or "") + ''
wrapProgram $out/bin/tar --prefix PATH ":" "${gzip}/bin"
'';
});
# fixes "Fontconfig error: Cannot load default config file"
# from nixpkgs/pkgs/development/libraries/pipewire/default.nix
fontsConf = makeFontsConf {
fontDirectories = [ ];
};
myEnv = [
# TODO which of these are needed?
stdenv
bash
bashInteractive
coreutils
diffutils
glibcLocales # TODO even on mac?
tree
tarWithGzip
gnugrep
gnused
gawk
curl
cacert # for curl https
fontconfig.lib # for R plotting scripts
];
# TODO why is patching shebangs on the wrapped scripts necessary??
mkModule = src: extraRunDeps: extraWraps:
let name = "OrthoLang-" + baseNameOf src;
runDeps = lib.lists.unique (myEnv ++ extraRunDeps);
in stdenv.mkDerivation {
inherit src name extraRunDeps extraWraps;
NIX_LDFLAGS = "-lfontconfig"; # for R plotting scripts
buildInputs = [ makeWrapper ] ++ runDeps;
installPhase = ''
source ${stdenv}/setup
mkdir -p $out/bin
for script in $src/*; do
base="$(basename "$script")"
dest="$out/bin/$base"
substituteAll $script $dest
chmod +x $dest
wrapProgram $dest \
--prefix PATH : "${pkgs.lib.makeBinPath runDeps}" ${extraWraps} \
--set NIX_SSL_CERT_FILE "${cacert}/etc/ssl/certs/ca-bundle.crt" \
--set FONTCONFIG_FILE "${fontsConf}"
done
'';
# problem: https://github.com/NixOS/nixpkgs/issues/11133
# solution: https://github.com/NixOS/nixpkgs/pull/74942
fixupPhase = if stdenv.isDarwin then ''
for script in $out/bin/.*-wrapped; do
patchShebangs "$script"
substituteInPlace $script --replace "#!/nix" "#!/usr/bin/env /nix"
done
'' else ''
for script in $out/bin/.*-wrapped; do
patchShebangs $script
done
'';
};
in rec {
myBlast = ncbi-blast; # for swapping it out if needed
# TODO remove these in favor of buildPythonPath!
myPy2Wrap = "--prefix PYTHONPATH : \"$out/bin:${myPy2.python.sitePackages}\"";
myPy3Wrap = "--prefix PYTHONPATH : \"$out/bin:${python36.python.sitePackages}\"";
myPy2 = python27.buildEnv.override {
# see https://github.com/NixOS/nixpkgs/issues/22319
ignoreCollisions = true;
extraLibs = with python27Packages; [
biopython
numpy
scipy
];
};
myR = rWrapper.override { packages = with rPackages; [
dplyr
ggplot2
readr
tidyr
UpSetR
VennDiagram
biomartr
data_table
futile_logger
];};
ortholang-biomartr = mkModule ./OrthoLang/Modules/BioMartR [ myR ] "";
ortholang-blasthits = mkModule ./OrthoLang/Modules/BlastHits [ myR ] "";
ortholang-blastrbh = mkModule ./OrthoLang/Modules/BlastRBH [ myR ] "";
ortholang-plots = mkModule ./OrthoLang/Modules/Plots [ myR ] "";
ortholang-setstable = mkModule ./OrthoLang/Modules/SetsTable [ myR ] "";
ortholang-range = mkModule ./OrthoLang/Modules/Range [ myR ] "";
ortholang-blast = mkModule ./OrthoLang/Modules/Blast [ myBlast ] "";
ortholang-blastdb = mkModule ./OrthoLang/Modules/BlastDB [ myBlast blastdbget ] "";
ortholang-crbblast = mkModule ./OrthoLang/Modules/CRBBlast [ crb-blast ] "";
ortholang-diamond = mkModule ./OrthoLang/Modules/Diamond [ diamond ] "";
ortholang-hmmer = mkModule ./OrthoLang/Modules/Hmmer [ myPy2 hmmer ] myPy2Wrap;
ortholang-mmseqs = mkModule ./OrthoLang/Modules/MMSeqs [ mmseqs2 ] "";
ortholang-muscle = mkModule ./OrthoLang/Modules/Muscle [ muscle ] "";
ortholang-psiblast = mkModule ./OrthoLang/Modules/PsiBlast [ myBlast ] "";
# TODO should the wrap not be necessary?
ortholang-seqio = mkModule ./OrthoLang/Modules/SeqIO [ myPy2 ] myPy2Wrap;
ortholang-orthofinder = mkModule ./OrthoLang/Modules/OrthoFinder [ myPy2 myBlast diamond orthofinder mcl fastme ] myPy2Wrap;
ortholang-sonicparanoid = mkModule ./OrthoLang/Modules/SonicParanoid [ sonicparanoid ] myPy3Wrap;
ortholang-treecl = mkModule ./OrthoLang/Modules/TreeCl [ myPy2 treeCl ] myPy2Wrap;
# ortholang-justorthologs = mkModule ./OrthoLang/Modules/JustOrthologs [ justorthologs ] "";
# this config file is only a template; it needs to be completed by busco.sh at runtime
ortholang-busco = mkModule ./OrthoLang/Modules/Busco
[ myBlast hmmer busco python36 which tarWithGzip ]
"--set BUSCO_CONFIG_FILE ${busco}/config/config.ini";
ortholang-load = mkModule ./OrthoLang/Modules/Load [ curl ] "";
ortholang-orthogroups = mkModule ./OrthoLang/Modules/OrthoGroups [ python36 ] "";
ortholang-greencut = mkModule ./OrthoLang/Modules/GreenCut [ myPy2 ] myPy2Wrap;
modules = [
ortholang-biomartr
ortholang-blast
ortholang-blastdb
ortholang-blasthits
ortholang-blastrbh
ortholang-crbblast
ortholang-diamond
ortholang-hmmer
ortholang-mmseqs
ortholang-muscle
ortholang-orthofinder
ortholang-plots
ortholang-setstable
ortholang-psiblast
ortholang-seqio
# ortholang-sonicparanoid
# ortholang-treecl
# ortholang-justorthologs
ortholang-busco
ortholang-load
ortholang-range
ortholang-orthogroups
ortholang-greencut
];
runDepends = modules ++ myEnv;
# TODO separate list of useful, non-conflicting programs to put on PATH?
}