diff options
Diffstat (limited to 'pkgs/applications/science')
6 files changed, 64 insertions, 15 deletions
diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix index 4bb3c7b34fe..cc6af8a17c0 100644 --- a/pkgs/applications/science/astronomy/gildas/default.nix +++ b/pkgs/applications/science/astronomy/gildas/default.nix @@ -1,14 +1,14 @@ -{ stdenv, fetchurl, gtk2-x11 , pkgconfig , python27 , gfortran , lesstif -, cfitsio , getopt , perl , groff , which, darwin +{ stdenv, fetchurl, gtk2-x11 , pkgconfig , python3 , gfortran , lesstif +, cfitsio , getopt , perl , groff , which, darwin, ncurses }: let - python27Env = python27.withPackages(ps: with ps; [ numpy ]); + python3Env = python3.withPackages(ps: with ps; [ numpy ]); in stdenv.mkDerivation rec { - srcVersion = "dec19a"; - version = "20191201_a"; + srcVersion = "jan20a"; + version = "20200101_a"; pname = "gildas"; src = fetchurl { @@ -16,17 +16,19 @@ stdenv.mkDerivation rec { # source code of the previous release to a different directory urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz" "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ]; - sha256 = "0kwq5gzgzx5hkbabwvbrw2958pqz4m2s501k5cbllgxh4sqp86b1"; + sha256 = "12n08pax7gwg2z121ix3ah5prq3yswqnf2yc8jgs4i9rgkpbsfzz"; }; - enableParallelBuilding = true; + # Python scripts are not converted to Python 3 syntax when parallel + # building is turned on. Disable it until this is fixed upstream. + enableParallelBuilding = false; nativeBuildInputs = [ pkgconfig groff perl getopt gfortran which ]; - buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ] + buildInputs = [ gtk2-x11 lesstif cfitsio python3Env ncurses ] ++ stdenv.lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ CoreFoundation ]); - patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ]; + patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ./imager-py3.patch ]; NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isClang "-Wno-unused-command-line-argument"; @@ -34,7 +36,7 @@ stdenv.mkDerivation rec { configurePhase='' substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out - substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python27Env} + substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python3Env} substituteInPlace utilities/main/gag-makedepend.pl --replace '/usr/bin/perl' ${perl}/bin/perl source admin/gildas-env.sh -c gfortran -o openmp echo "gag_doc: $out/share/doc/" >> kernel/etc/gag.dico.lcl diff --git a/pkgs/applications/science/astronomy/gildas/imager-py3.patch b/pkgs/applications/science/astronomy/gildas/imager-py3.patch new file mode 100644 index 00000000000..71a129164ba --- /dev/null +++ b/pkgs/applications/science/astronomy/gildas/imager-py3.patch @@ -0,0 +1,12 @@ +diff -ruN gildas-src-jan20a.orig/contrib/imager/pro/define.ima gildas-src-jan20a/contrib/imager/pro/define.ima +--- gildas-src-jan20a.orig/contrib/imager/pro/define.ima 2020-01-01 02:15:16.000000000 +0100 ++++ gildas-src-jan20a/contrib/imager/pro/define.ima 2020-01-14 11:18:46.000000000 +0100 +@@ -9,7 +9,7 @@ + ! + ! Patch for a Bug on Mac-OS/X where Python blocks if activated first + ! from a script launched by a widget. +-python print "Starting Python" ++python print("Starting Python") + ! + ! INPUT, GO and UVT_CONVERT always defined by GreG + define command GO "@ p_go.ima" gag_pro:go_greg.hlp diff --git a/pkgs/applications/science/biology/manta/default.nix b/pkgs/applications/science/biology/manta/default.nix new file mode 100644 index 00000000000..f0f0575e055 --- /dev/null +++ b/pkgs/applications/science/biology/manta/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, zlib, python2 }: + +stdenv.mkDerivation rec { + pname = "manta"; + version = "1.6.0"; + + src = fetchFromGitHub { + owner = "Illumina"; + repo = "manta"; + rev = "v${version}"; + sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib python2 ]; + postFixup = '' + sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py + sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py + sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py + ''; + doInstallCheck = true; + installCheckPhase = '' + rm $out/lib/python/**/*.pyc + PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript' + PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow' + ''; + + meta = with stdenv.lib; { + description = "Structural variant caller"; + license = licenses.gpl3; + homepage = "https://github.com/Illumina/manta"; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index a67653c8437..44247f294aa 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.21.3"; + version = "2.21.6"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0s1gn2bkya41866kd8zj0g8xjbivs763jqmlzdpjz4c25h6xkhns"; + sha256 = "1vpyzhrs3bbviwk2n7k5296rnsw7g9ksvjsibl0gm7dawip9jb5s"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index daa2925de7c..f2c5e9f25be 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.9"; + version = "1.10"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"; + sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"; }; nativeBuildInputs = [ perl ]; diff --git a/pkgs/applications/science/logic/cubicle/default.nix b/pkgs/applications/science/logic/cubicle/default.nix index cd41e1ca64b..d198de41f9b 100644 --- a/pkgs/applications/science/logic/cubicle/default.nix +++ b/pkgs/applications/science/logic/cubicle/default.nix @@ -19,6 +19,6 @@ stdenv.mkDerivation rec { homepage = http://cubicle.lri.fr/; license = licenses.asl20; platforms = platforms.unix; - maintainers = with maintainers; [ lucas8 ]; + maintainers = with maintainers; [ dwarfmaster ]; }; } |