From 4c6a34535b58d1470bd3c06e388ccbdc1503a1fe Mon Sep 17 00:00:00 2001 From: Tyson Whitehead Date: Thu, 21 Jan 2021 11:52:46 -0500 Subject: [PATCH] blast, minia, pythonPackages.vtk: Upstream now --- pkgs/all-packages.nix | 7 ---- pkgs/blast/default.nix | 74 ---------------------------------------- pkgs/blast/install.patch | 16 --------- pkgs/minia.nix | 30 ---------------- pkgs/python-packages.nix | 5 --- 5 files changed, 132 deletions(-) delete mode 100644 pkgs/blast/default.nix delete mode 100644 pkgs/blast/install.patch delete mode 100644 pkgs/minia.nix diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix index f54a44a..cefa780 100644 --- a/pkgs/all-packages.nix +++ b/pkgs/all-packages.nix @@ -4,11 +4,6 @@ # self: super: pkgs: with pkgs; { - blast = callPackage ./blast { - stdenv = overrideCC stdenv gcc5; - boost = boost162; - }; - cloudcompare = libsForQt5.callPackage ./cloudcompare.nix { boost = boost15x; }; fastqc = callPackage ./fastqc.nix { }; @@ -26,8 +21,6 @@ self: super: pkgs: with pkgs; { mfixgui = python36Packages.callPackage ./mfix/mfixgui.nix { }; mfixsolver = callPackage ./mfix/mfixsolver.nix { }; - minia = callPackage ./minia.nix { }; - inherit (callPackage ./opengl/default.nix { inherit super; }) libGL mesa_glxgallium; openfoam = callPackage ./openfoam { stdenv = overrideCC stdenv gcc7; }; diff --git a/pkgs/blast/default.nix b/pkgs/blast/default.nix deleted file mode 100644 index aa0fd6e..0000000 --- a/pkgs/blast/default.nix +++ /dev/null @@ -1,74 +0,0 @@ -{ stdenv, fetchurl, cpio, curl -, python, perl, zlib, bzip2, boost }: - -stdenv.mkDerivation rec { - version = "2.6.0"; - name = "ncbi-blast-${version}"; - - src = fetchurl { - url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz"; - sha256 = "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"; - }; - - # The install target is broken as it tries to install a subdirectory using install - patches = [ ./install.patch ]; - - # Contains a lot of hardcoded paths for standard utils and some scripts the just reset PATH for the fun of it. - # - # - for every $cmd on the path, replace all occurances of /usr/bin/$cmd and /bin/$cmd with it - # - delete every line that has PATH=/bin:/usr/bin in it - # - # A bit of prefix/suffix matching and escaping is required for the first to avoid replacing things like $(foo)/bin/... - # and keeping the sed regexps valid in the face of commands like [. - # - postPatch = '' - patchShebangs . - echo 'replacing hardcoded /bin and /usr/bin commands with any nix equivalents on the PATH' - find -L ''${PATH//:/ } -maxdepth 1 -type f -perm -u=x -print0 | - while read -d ''' -r cmd; do - cmd=''${cmd//\/\\\\} - cmd=''${cmd//{/\\{} - cmd=''${cmd//[/\\[} - cmd=''${cmd//(/\\(} - cmd=''${cmd//)/\\)} - cmd=''${cmd//+/\\+} - cmd=''${cmd//\*/\\*} - cmd=''${cmd//\?/\\?} - cmd=''${cmd//!/\\!} - echo 's!(^|[[:space:]({>`'\'''";|,=@\!]|&&|\|\|)(/usr)?/bin/'"''${cmd##*/}"'($|[[:space:])}<`'\'''";|,]|&&|\|\|)!\1'"$cmd"'\3!g' - done >> commands.sed - find c++ -type f -print0 | xargs -0 -n 16 -P $NIX_BUILD_CORES \ - sed -i -E \ - -e '/ *PATH=['\'''"]?\/bin:\/usr\/bin/d' \ - -e 's!/bin/(\$base_action|\$LN_S)!\1!g' \ - -f commands.sed - ''; - - # AR command variable is abused to include parameters, but these don't get figured out if $AR is already set - preConfigure = '' - cd c++ - test -n "$AR" && AR="$AR cr" || true - ''; - - configureFlags = "--with-dll --without-debug --with-bin-release --with-strip --with-mt --without-opengl --without-connext"; - - buildInputs = [ - boost - zlib - bzip2 - cpio - curl - python -# python3 -- some scripts like ./c++/scripts/projects/magicblast/post_build/blast_utils.py - perl - ]; - - meta = with stdenv.lib; { - homepage = https://blast.ncbi.nlm.nih.gov/; - description = "BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance."; - platforms = platforms.all; - license = licenses.publicDomain; - }; - - enableParallelBuilding = true; -} diff --git a/pkgs/blast/install.patch b/pkgs/blast/install.patch deleted file mode 100644 index 3fbd6c0..0000000 --- a/pkgs/blast/install.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- ncbi-blast-2.6.0+-src/c++/src/build-system/Makefile.in.top_ 2018-04-23 16:13:57.759988900 -0400 -+++ ncbi-blast-2.6.0+-src/c++/src/build-system/Makefile.in.top 2018-04-23 16:14:38.270252707 -0400 -@@ -49,9 +49,10 @@ - for x in *.a; do \ - $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \ - done -- cd $(includedir0) && find * -name CVS -prune -o -print |\ -- cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ cd $(includedir0) && find * -type f \( -name '*.inl' -o -name '*.h' -o -name '*.hpp' -o -name '*.c' \) \ -+ -exec $(INSTALL) -m 644 -D \{\} $(pincludedir)/\{\} \; -+ cd $(incdir) && find * -type f \( -name '*.inl' -o -name '*.h' -o -name '*.hpp' -o -name '*.c' \) \ -+ -exec $(INSTALL) -m 644 -D \{\} $(pincludedir)/\{\} \; - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/pkgs/minia.nix b/pkgs/minia.nix deleted file mode 100644 index 1acee53..0000000 --- a/pkgs/minia.nix +++ /dev/null @@ -1,30 +0,0 @@ -{ stdenv, fetchFromGitHub, cmake, zlib }: - -stdenv.mkDerivation rec { - name = "minia-${version}"; - version = "3.2.0"; - - src = fetchFromGitHub { - owner = "GATB"; - repo = "minia"; - fetchSubmodules = true; - rev = "v${version}"; - sha256 = "1kziky9hgys3fp8891vx2hskwg7zw49fbnq9zvc7pwmc7qskasli"; - }; - - buildInputs = [ - cmake - zlib - ]; - - hardeningDisable = [ "format" ]; - - meta = with stdenv.lib; { - description = "A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day."; - homepage = https://github.com/GATB/minia; - platforms = platforms.all; - license = licenses.gpl3; - }; - - enableParallelBuilding = true; -} diff --git a/pkgs/python-packages.nix b/pkgs/python-packages.nix index 31f4fd4..e40f71f 100644 --- a/pkgs/python-packages.nix +++ b/pkgs/python-packages.nix @@ -10,10 +10,5 @@ pkgs: self: super: with self; { pybedtools = callPackage ./pybedtools.nix { }; - vtk = disabledIf (!(pythonOlder "3.7")) ( toPythonModule ( pkgs.vtk.overrideAttrs ( attrs: { - cmakeFlags = attrs.cmakeFlags or [] ++ [ "-DVTK_WRAP_PYTHON:BOOL=ON" ]; - buildInputs = attrs.buildInputs or [] ++ [ python ]; - } ) ) ); - xopen = callPackage ./xopen.nix { }; }