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Merge pull request #171469 from luispedro/static_bioinformatics

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Ben Siraphob 2022-05-04 20:36:26 -06:00 committed by GitHub
commit 1bb17332ab
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4 changed files with 31 additions and 3 deletions
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2
pkgs/applications/science/biology/bwa/default.nix
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@ -17,6 +17,8 @@ stdenv.mkDerivation rec {
sed -i '/^CC/d' Makefile
'';
makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
# it's unclear which headers are intended to be part of the public interface
# so we may find ourselves having to add more here over time
installPhase = ''

3
pkgs/applications/science/biology/megahit/default.nix
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@ -14,6 +14,9 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib ];
cmakeFlags = lib.optional stdenv.hostPlatform.isStatic [
"-DSTATIC_BUILD=ON"
];
meta = with lib; {
description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph";
license = licenses.gpl3;

9
pkgs/applications/science/biology/samtools/default.nix
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@ -22,8 +22,15 @@ stdenv.mkDerivation rec {
buildInputs = [ zlib ncurses htslib ];
preConfigure = lib.optional stdenv.hostPlatform.isStatic ''
export LIBS="-lz -lbz2 -llzma"
'';
makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
configureFlags = [ "--with-htslib=${htslib}" ]
++ lib.optional (ncurses == null) "--without-curses";
++ lib.optional (ncurses == null) "--without-curses"
++ lib.optional stdenv.hostPlatform.isStatic ["--without-curses" ]
;
preCheck = ''
patchShebangs test/

20
pkgs/development/libraries/science/biology/htslib/default.nix
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@ -14,9 +14,25 @@ stdenv.mkDerivation rec {
buildInputs = [ zlib bzip2 xz curl ];
configureFlags = [ "--enable-libcurl" ]; # optional but strongly recommended
configureFlags = if ! stdenv.hostPlatform.isStatic
then [ "--enable-libcurl" ] # optional but strongly recommended
else [ "--disable-libcurl" "--disable-plugins" ];
installFlags = [ "prefix=$(out)" ];
# In the case of static builds, we need to replace the build and install phases
buildPhase = lib.optional stdenv.hostPlatform.isStatic ''
make AR=$AR lib-static
make LDFLAGS=-static bgzip htsfile tabix
'';
installPhase = lib.optional stdenv.hostPlatform.isStatic ''
install -d $out/bin
install -d $out/lib
install -d $out/include/htslib
install -D libhts.a $out/lib
install -m644 htslib/*h $out/include/htslib
install -D bgzip htsfile tabix $out/bin
'';
preCheck = ''
patchShebangs test/