blast, minia, pythonPackages.vtk: Upstream now

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; };

pkgs/blast/default.nix

@@ -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;
-}

pkgs/blast/install.patch

@@ -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:

pkgs/minia.nix

@@ -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;
-}

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 { };
 }