Fix rendering of more packages (#15245)

* Fix rendering of more packages * update recipes * A few updates * last probably fails still * merge master * fix last/874 * last probably doesn't need python for building
bioconda · May 12, 2019 · 38ac254 · 38ac254
1 parent dd67a62
commit 38ac254
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -1,3 +1,6 @@
+# last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
+recipes/last/638
+
 # Timeout downloading from sourceforge
 recipes/transcomb
 
@@ -70,7 +73,6 @@ recipes/htseq/0.7.2
 recipes/htseq/0.9.1
 recipes/freebayes/1.1.0.46
 recipes/mothur/1.36.1
-recipes/samtools/1.1
 recipes/blast/2.2.21
 recipes/blast-legacy/2.2.22
 recipes/fwdpp/0.5.3

diff --git a/recipes/gromacs/2018/meta.yaml b/recipes/gromacs/2018/meta.yaml
@@ -1,23 +1,17 @@
-about:
-  home: http://www.gromacs.org/
-  license: GNU Lesser General Public License (LGPL)
-  summary: GROMACS is a versatile package to perform molecular dynamics.
-
 package:
   name: gromacs
   version: 2018.6
 
-build:
-  number: 0
-
 # See http://manual.gromacs.org/documentation/
 # for latest release. Note that version scheme changed from
 # 5.1 to 2016.x and 2018.x
 source:
   url: http://ftp.gromacs.org/pub/gromacs/gromacs-2018.6.tar.gz
-  md5: 997f2b8108197780d61b23b5eb05644a
   sha256: 94b0dbafe7b29a0fe509099caa4fc075e616eb0d6ab4a785c7072fd1b2c5aba0
 
+build:
+  number: 1
+
 requirements:
   build:
     - {{ compiler('cxx') }}
@@ -39,6 +33,10 @@ test:
   commands:
     - gmx -version
 
+about:
+  home: http://www.gromacs.org/
+  license: GNU Lesser General Public License (LGPL)
+  summary: GROMACS is a versatile package to perform molecular dynamics.
 
 extra:
   identifiers:

diff --git a/recipes/gromacs/2019/meta.yaml b/recipes/gromacs/2019/meta.yaml
@@ -3,26 +3,18 @@
 # http://manual.gromacs.org/documentation/
 {% set name = "gromacs" %}
 {% set version = "2019.1" %}
-{% set md5 = "dccfadda6a7d4ab80fcb4059606a4ef3" %}
 # Calculate manually
 {% set sha256 = "b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec" %}
 
-
-about:
-  home: http://www.gromacs.org/
-  license: GNU Lesser General Public License (LGPL)
-  summary: GROMACS is a versatile package to perform molecular dynamics.
-
 package:
   name: gromacs
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
 
 source:
   url: http://ftp.gromacs.org/pub/gromacs/gromacs-{{ version }}.tar.gz
-  md5: {{ md5 }}
   sha256: {{ sha256 }}
 
 requirements:
@@ -49,6 +41,10 @@ test:
   commands:
     - gmx -version
 
+about:
+  home: http://www.gromacs.org/
+  license: GNU Lesser General Public License (LGPL)
+  summary: GROMACS is a versatile package to perform molecular dynamics.
 
 extra:
   identifiers:

diff --git a/recipes/kat/2.0.8/meta.yaml b/recipes/kat/2.0.8/meta.yaml
@@ -1,20 +1,19 @@
-about:
-  home: https://github.com/TGAC/KAT/
-  license: 'GPL3'
-  license_file: 'COPYING'
-  summary: 'KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts'
-
-build:
-  number: 3
-  skip: True # [osx]
-
 package:
   name: kat
   version: '2.0.8'
 
+source:
+  url: https://github.com/TGAC/KAT/archive/Release-2.0.8.tar.gz
+  sha1: 76f8a5fba81837dd20d00eaefb3709da476c1ca6
+
+build:
+  number: 4
+  skip: True # [osx]
+
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - autoconf
     - automake
     - libtool
@@ -28,14 +27,16 @@ requirements:
     - gnuplot
     - jellyfish
 
-source:
-  url: https://github.com/TGAC/KAT/archive/Release-2.0.8.tar.gz
-  sha1: 76f8a5fba81837dd20d00eaefb3709da476c1ca6
-
 test:
   commands:
     - kat --version
 
+about:
+  home: https://github.com/TGAC/KAT/
+  license: 'GPL3'
+  license_file: 'COPYING'
+  summary: 'KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts'
+
 extra:
   identifiers:
     - biotools:KAT
diff --git a/recipes/last/490/build.sh b/recipes/last/490/build.sh
@@ -22,7 +22,7 @@ last-dotplot \
 
 for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done
 
-make
+make CXX=${CXX} CC=${CC}
 
 mkdir -p $PREFIX/bin
 for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done

diff --git a/recipes/last/490/meta.yaml b/recipes/last/490/meta.yaml
@@ -1,8 +1,3 @@
-about:
-  home: 'http://last.cbrc.jp/'
-  license: GPLv3
-  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
-
 package:
   name: last
   version: '490'
@@ -15,13 +10,12 @@ source:
     - last-pair-probs.23patch
 
 build:
-  number: 3
+  number: 4
 
 requirements:
   build:
     - {{ compiler('cxx') }}
-  host:
-    - python
+    - {{ compiler('c') }}
   run:
     - python
 
@@ -34,6 +28,11 @@ test:
     - "last-merge-batches -V"
     - "maf-convert -h"
 
+about:
+  home: 'http://last.cbrc.jp/'
+  license: GPLv3
+  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
+
 extra:
   identifiers:
     - biotools:last
diff --git a/recipes/last/638/build.sh b/recipes/last/638/build.sh
@@ -23,7 +23,7 @@ last-dotplot \
 for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done
 
 chmod +x $SRC_DIR/build/*
-make
+make CXX=${CXX} CC=${CC}
 
 mkdir -p $PREFIX/bin
 for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done

diff --git a/recipes/last/638/meta.yaml b/recipes/last/638/meta.yaml
@@ -1,8 +1,3 @@
-about:
-  home: 'http://last.cbrc.jp/'
-  license: GPLv3
-  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
-
 package:
   name: last
   version: '638'
@@ -14,11 +9,12 @@ source:
     - maf-convert.23patch
 
 build:
-  number: 6
+  number: 7
 
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - python
   run:
@@ -33,6 +29,11 @@ test:
     - "last-merge-batches -V"
     - "maf-convert -h"
 
+about:
+  home: 'http://last.cbrc.jp/'
+  license: GPLv3
+  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
+
 extra:
   identifiers:
     - biotools:last
diff --git a/recipes/last/874/build.sh b/recipes/last/874/build.sh
@@ -23,15 +23,12 @@ last-map-probs \
 last-dotplot \
 "
 
-if [[ $(uname) == "Darwin" ]]; then
-	export CMAKE_CXX_FLAGS="-stdlib=libc++"
-fi
-
 for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done
 
 chmod +x $SRC_DIR/build/*
-export LIBRARY_PATH=${PREFIX}/lib
-make CXX="g++ $CMAKE_CXX_FLAGS -L${PREFIX}/lib"
+pushd src
+make CXX="$CXX" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib -lz"
+popd
 
 mkdir -p $PREFIX/bin
 for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done

diff --git a/recipes/last/874/meta.yaml b/recipes/last/874/meta.yaml
@@ -1,8 +1,3 @@
-about:
-  home: 'http://last.cbrc.jp/'
-  license: GPLv3
-  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
-
 package:
   name: last
   version: '874'
@@ -14,18 +9,18 @@ source:
     - maf-convert.23patch
 
 build:
-  number: 1
-  skip: False
+  number: 2
 
 requirements:
   build:
     - {{ compiler('cxx') }}
     - {{ compiler('c') }}
   host:
-    - python
+    - zlib
   run:
     - python
     - future
+    - zlib
 
 test:
   commands:
@@ -38,6 +33,11 @@ test:
     - "last-merge-batches -V"
     - "maf-convert -h"
 
+about:
+  home: 'http://last.cbrc.jp/'
+  license: GPLv3
+  summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)."
+
 extra:
   identifiers:
     - biotools:last
diff --git a/recipes/last/build.sh b/recipes/last/build.sh
@@ -11,5 +11,5 @@ then
 fi
 
 cp ${SRC_DIR}/scripts/* ${PREFIX}/bin/
-make install CXX="g++ $CMAKE_CXX_FLAGS -I$PREFIX/include -L$PREFIX/lib" prefix=${PREFIX}
+make install CXX="${CXX} $CMAKE_CXX_FLAGS -I$PREFIX/include -L$PREFIX/lib" prefix=${PREFIX}
 chmod +x ${PREFIX}/bin/*
diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml
@@ -11,14 +11,14 @@ source:
   url: http://last.cbrc.jp/{{ name|lower }}-{{ version }}.zip
 
 build:
-  number: 0
+  number: 1
 
 requirements:
   build:
     - {{ compiler('c') }}
-    - zlib
+    - {{ compiler('cxx') }}
   host:
-    - python
+    - zlib
   run:
     - zlib
     - python

diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml
@@ -1,15 +1,14 @@
-about:
-  home: https://github.com/samtools/samtools
-  license: MIT
-  summary: Tools for dealing with SAM and BAM files
-
-build:
-  number: 5
-
 package:
   name: samtools
   version: 0.1.19
 
+source:
+  sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4
+  url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2
+
+build:
+  number: 6
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -20,14 +19,15 @@ requirements:
     - ncurses
     - zlib
 
-source:
-  sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4
-  url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2
-
 test:
   commands:
     - "samtools view --help 2>&1 | grep Notes"
 
+about:
+  home: https://github.com/samtools/samtools
+  license: MIT
+  summary: Tools for dealing with SAM and BAM files
+
 extra:
   identifiers:
     - biotools:samtools
diff --git a/recipes/samtools/1.1/build.sh b/recipes/samtools/1.1/build.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 sed -i.bak -e 's/-lcurses/-lncurses/' Makefile
 sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile
-make
+make CC=${CC} CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib"
 mkdir -p $PREFIX/bin
 mv samtools $PREFIX/bin