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author | Vladimír Čunát <vcunat@gmail.com> | 2018-01-27 09:14:22 +0100 |
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committer | Vladimír Čunát <vcunat@gmail.com> | 2018-01-27 09:14:22 +0100 |
commit | 2d2dbe083f0df9dbde5643234cb2b067653739fa (patch) | |
tree | 66195da25376f3bb7bed16d469d85fcaffe0f13b /pkgs/applications/science | |
parent | ef60e411455c9d7ef16069df63daf2c9fbd66ec6 (diff) | |
parent | 9c95eb828ab6cc7b022197f68e1e0a8ce4241d89 (diff) | |
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Merge branch 'master' into staging
Hydra: ?compare=1429281
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 156 insertions, 33 deletions
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index a2a40f0acc80..13cb407391c0 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "igv-${version}"; - version = "2.3.98"; + version = "2.4.6"; src = fetchurl { - url = "http://data.broadinstitute.org/igv/projects/downloads/IGV_${version}.zip"; - sha256 = "1bjdsvx8jsbcry6v7yfclh3vrlsvaw38f3s9587lklj63zj638l2"; + url = "http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip"; + sha256 = "00p9xhfn6snzm31q9l3dxccsj7rhlci8n3pgpy3k67q91mi2hkna"; }; buildInputs = [ unzip jre ]; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix new file mode 100644 index 000000000000..d80ffea9a780 --- /dev/null +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchFromGitHub, cmake, hdf5, zlib }: + +stdenv.mkDerivation rec { + name = "kallisto-${version}"; + version = "0.43.1"; + + src = fetchFromGitHub { + repo = "kallisto"; + owner = "pachterlab"; + rev = "v${version}"; + sha256 = "04697pf7jvy7vw126s1rn09q4iab9223jvb1nb0jn7ilwkq7pgwz"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ hdf5 zlib ]; + + meta = with stdenv.lib; { + description = "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"; + homepage = https://pachterlab.github.io/kallisto; + license = licenses.bsd2; + platforms = platforms.linux; + maintainers = [ maintainers.arcadio ]; + }; +} diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 24dc4436b0fd..686e93b5d5e2 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -18,6 +18,7 @@ # - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath { stdenv +, bash , fetchurl , perl , gfortran @@ -26,13 +27,17 @@ , gettext , which , texlive +, texinfo , hevea }: stdenv.mkDerivation rec { - version = "8.0"; + version = "8.1"; name = "sage-${version}"; + # Modified version of patchShebangs that patches to the sage-internal version if possible + # and falls back to the system version if not. + patchSageShebangs = ./patchSageShebangs.sh; src = fetchurl { # Note that the source is *not* fetched from github, since that doesn't # the upstream folder with all the source tarballs of the spkgs. @@ -70,11 +75,12 @@ stdenv.mkDerivation rec { "http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz" "http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz" ]; - sha256 = "1a9rhb8jby6fdqa2s7n2fl9jwqqlsl7qz7dbpbwvg6jwlrvni7fg"; + sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq"; }; postPatch = '' substituteAllInPlace src/bin/sage-env + bash=${bash} substituteAllInPlace build/bin/sage-spkg ''; installPhase = '' @@ -84,14 +90,16 @@ stdenv.mkDerivation rec { outputs = [ "out" "doc" ]; buildInputs = [ + bash # needed for the build perl # needed for the build python # needed for the build - gfortran # needed to build giac + gfortran # needed to build giac, openblas autoreconfHook # needed to configure sage with prefix gettext # needed to build the singular spkg hevea # needed to build the docs of the giac spkg which # needed in configure of mpir # needed to build the docs of the giac spkg + texinfo # needed to build maxima (texlive.combine { inherit (texlive) scheme-basic collection-pstricks # needed by giac @@ -102,18 +110,22 @@ stdenv.mkDerivation rec { }) ]; + nativeBuildInputs = [ gfortran perl which ]; + patches = [ # fix usages of /bin/rm ./spkg-singular.patch # help python find the crypt library - ./spkg-python2.patch - ./spkg-python3.patch + # patches python3 and indirectly python2, since those installation files are symlinked + ./spkg-python.patch # fix usages of /usr/bin/perl ./spkg-git.patch # fix usages of /bin/cp and add necessary argument to function call ./spkg-giac.patch # environment ./env.patch + # adjust wrapper shebang and patch shebangs after each spkg build + ./shebangs.patch ]; enableParallelBuilding = true; @@ -144,7 +156,14 @@ stdenv.mkDerivation rec { preBuild = '' # TODO do this conditionally export SAGE_SPKG_INSTALL_DOCS='no' - patchShebangs build + # symlink python to make sure the shebangs are patched to the sage path + # while still being able to use python before building it + # (this is important because otherwise sage will try to install python + # packages globally later on) + ln -s "${python}/bin/python2" $out/bin/python2 + ln -s "$out/bin/python2" $out/bin/python + touch $out/bin/python3 + bash $patchSageShebangs . ''; postBuild = '' @@ -153,9 +172,12 @@ stdenv.mkDerivation rec { rm -rf "$out/sage-root/src/.git" rm -r "$out/sage-root/logs" # Fix dependency cycle between out and doc + rm -f "$out/sage-root/config.log" rm -f "$out/sage-root/config.status" rm -f "$out/sage-root/build/make/Makefile-auto" rm -f "$out/sage-home/.sage/gap/libgap-workspace-"* + # Make sure all shebangs are properly patched + bash $patchSageShebangs $out ''; # TODO there are some doctest failures, which seem harmless. diff --git a/pkgs/applications/science/math/sage/patchSageShebangs.sh b/pkgs/applications/science/math/sage/patchSageShebangs.sh new file mode 100644 index 000000000000..6ddf93af0114 --- /dev/null +++ b/pkgs/applications/science/math/sage/patchSageShebangs.sh @@ -0,0 +1,51 @@ +# This is a slightly modified version of nix's default patchShebangs + +dir="$1" + +echo "patching sage internal script interpreter paths in $( readlink -f "$dir")" + +find "$dir" -type f -perm -0100 | while read f; do + if [ "$(head -1 "$f" | head -c+2)" != '#!' ]; then + # missing shebang => not a script + continue + fi + + oldInterpreterLine=$(head -1 "$f" | tail -c+3) + read -r oldPath arg0 args <<< "$oldInterpreterLine" + + if $(echo "$oldPath" | grep -q "/bin/env$"); then + # Check for unsupported 'env' functionality: + # - options: something starting with a '-' + # - environment variables: foo=bar + if $(echo "$arg0" | grep -q -- "^-.*\|.*=.*"); then + echo "unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)" + exit 1 + fi + executable="$arg0" + else + if [ "$oldPath" = "" ]; then + # If no interpreter is specified linux will use /bin/sh. Set + # oldpath="/bin/sh" so that we get /nix/store/.../sh. + oldPath="/bin/sh" + fi + executable="$(basename "$oldPath")" + args="$arg0 $args" + fi + + newPath="$(echo "$out/bin/$executable $args" | sed 's/[[:space:]]*$//')" + if [[ ! -x "$newPath" ]] ; then + newPath="$(command -v "$executable" || true)" + fi + + # Strip trailing whitespace introduced when no arguments are present + newInterpreterLine="$(echo "$newPath $args" | sed 's/[[:space:]]*$//')" + + if [ -n "$oldPath" -a "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]; then + if [ -n "$newPath" -a "$newPath" != "$oldPath" ]; then + echo "$f: sage interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\"" + # escape the escape chars so that sed doesn't interpret them + escapedInterpreterLine=$(echo "$newInterpreterLine" | sed 's|\\|\\\\|g') + sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f" + fi + fi +done diff --git a/pkgs/applications/science/math/sage/shebangs.patch b/pkgs/applications/science/math/sage/shebangs.patch new file mode 100644 index 000000000000..96ed5a4bc6c3 --- /dev/null +++ b/pkgs/applications/science/math/sage/shebangs.patch @@ -0,0 +1,36 @@ +diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg +index 83e61a7e0d..942ba206c7 100755 +--- a/build/bin/sage-spkg ++++ b/build/bin/sage-spkg +@@ -648,8 +648,12 @@ if ! sage-apply-patches; then + error_msg "Error applying patches" + exit 1 + fi ++ ++@bash@/bin/bash @patchSageShebangs@ . ++ + cd .. + ++ + ################################################################## + # The package has been extracted, prepare for installation + ################################################################## +@@ -671,7 +675,7 @@ write_script_wrapper() { + local tmpscript="$(dirname "$script")/.tmp-${script##*/}" + + cat > "$tmpscript" <<__EOF__ +-#!/usr/bin/env bash ++#! @bash@/bin/bash + + export SAGE_ROOT="$SAGE_ROOT" + export SAGE_SRC="$SAGE_SRC" +@@ -833,6 +837,9 @@ if [ "$UNAME" = "CYGWIN" ]; then + sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null + fi + ++@bash@/bin/bash @patchSageShebangs@ . ++@bash@/bin/bash @patchSageShebangs@ "$out/bin" ++ + echo "Successfully installed $PKG_NAME" + + if [ "$SAGE_CHECK" = "yes" ]; then diff --git a/pkgs/applications/science/math/sage/spkg-python.patch b/pkgs/applications/science/math/sage/spkg-python.patch new file mode 100644 index 000000000000..e39981b6552a --- /dev/null +++ b/pkgs/applications/science/math/sage/spkg-python.patch @@ -0,0 +1,13 @@ +diff --git a/build/pkgs/python3/spkg-build b/build/pkgs/python3/spkg-build +index 56db087ae5..b450703c5f 100644 +--- a/build/pkgs/python3/spkg-build ++++ b/build/pkgs/python3/spkg-build +@@ -27,6 +27,8 @@ fi + export EXTRA_CFLAGS="`testcflags.sh -Wno-unused` $CFLAGS" + unset CFLAGS + ++export LDFLAGS="$LDFLAGS -lcrypt" ++ + if [ "$UNAME" = Darwin ]; then + PYTHON_CONFIGURE="--disable-toolbox-glue $PYTHON_CONFIGURE" + diff --git a/pkgs/applications/science/math/sage/spkg-python2.patch b/pkgs/applications/science/math/sage/spkg-python2.patch deleted file mode 100644 index 5d92d3f8beaf..000000000000 --- a/pkgs/applications/science/math/sage/spkg-python2.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- old/build/pkgs/python2/spkg-install 2017-07-21 14:10:00.000000000 -0500 -+++ new/build/pkgs/python2/spkg-install 2017-10-15 11:26:54.823134067 -0500 -@@ -22,6 +22,9 @@ - - cd src - -+LDFLAGS="-lcrypt $LDFLAGS" -+export LDFLAGS -+ - if [ "$SAGE_DEBUG" = "yes" ]; then - echo "Building Python with pydebug" - PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug" diff --git a/pkgs/applications/science/math/sage/spkg-python3.patch b/pkgs/applications/science/math/sage/spkg-python3.patch deleted file mode 100644 index 51827fd11be0..000000000000 --- a/pkgs/applications/science/math/sage/spkg-python3.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- old/build/pkgs/python3/spkg-install 2017-07-21 14:10:00.000000000 -0500 -+++ new/build/pkgs/python3/spkg-install 2017-10-15 13:11:17.769261404 -0500 -@@ -22,6 +22,9 @@ - - cd src - -+LDFLAGS="-lcrypt $LDFLAGS" -+export LDFLAGS -+ - if [ "$SAGE_DEBUG" = "yes" ]; then - echo "Building Python with pydebug" - PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug" |