diff --git a/build-fail-blacklist b/build-fail-blacklist index 42f8db807dcdb..c58937125e635 100644 --- 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}' 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 index 49a689c24a85c..e48e00cb279fb 100644 --- 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 index efafa104893fb..26c4513bab3f1 100644 --- 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 index 7fbca087dac59..c2b25ef1cdc84 100644 --- 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 index aadb4ff6d94d6..0e1cbe553e0fa 100644 --- 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 index e30832b4807ea..d5e3dd3ce4a90 100644 --- 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 index 6da6bf2a591b6..cae8657f76fc8 100644 --- 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 index a0db56fe99e96..a2083277a56da 100644 --- 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 index 995403d9d6a22..fd9dadd53acd8 100644 --- 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 index fbc7bfb961fd7..2600ae40eb6d9 100644 --- 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 index 64cddad981b08..a11acca9863db 100644 --- 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 ${PREFIX}/bin/* diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index fd833bb102871..bb191d2fe9d3b 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -11,14 +11,14 @@ source: url: http://last.cbrc.jp/{{ name|lower }}-{{ version }}.zip build: - number: 0 + number: 1 requirements: build: - {{ compiler('c') }} - - zlib + - {{ compiler('cxx') }} host: - - python + - zlib run: - zlib - python diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml index 70cad3a395dd9..0fbd7a0a6deef 100644 --- a/recipes/samtools/0.1.19/meta.yaml +++ b/recipes/samtools/0.1.19/meta.yaml @@ -1,15 +1,14 @@ -about: - home: https://github.com/samtools/samtools - license: MIT - summary: Tools for dealing with SAM and BAM files - -build: - number: 5 - package: name: samtools version: 0.1.19 +source: + sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 + url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2 + +build: + number: 6 + requirements: build: - {{ compiler('c') }} @@ -20,14 +19,15 @@ requirements: - ncurses - zlib -source: - sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 - url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2 - test: commands: - "samtools view --help 2>&1 | grep Notes" +about: + home: https://github.com/samtools/samtools + license: MIT + summary: Tools for dealing with SAM and BAM files + extra: identifiers: - biotools:samtools diff --git a/recipes/samtools/1.1/build.sh b/recipes/samtools/1.1/build.sh index bdfd59a3924f0..e6225bcfe1ac5 100644 --- a/recipes/samtools/1.1/build.sh +++ b/recipes/samtools/1.1/build.sh @@ -1,6 +1,6 @@ #!/bin/sh sed -i.bak -e 's/-lcurses/-lncurses/' Makefile sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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 diff --git a/recipes/samtools/1.1/meta.yaml b/recipes/samtools/1.1/meta.yaml index d5a3cf5f2e2d7..f66ee0382bba8 100644 --- a/recipes/samtools/1.1/meta.yaml +++ b/recipes/samtools/1.1/meta.yaml @@ -1,32 +1,33 @@ -about: - home: https://github.com/samtools/samtools - license: MIT - summary: Tools for dealing with SAM, BAM and CRAM files - -build: - number: 2 - package: name: samtools version: '1.1' +source: + sha256: c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 + url: http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2 + +build: + number: 3 + requirements: build: - - ncurses + - {{ compiler('c') }} host: - zlib + - ncurses run: - ncurses - zlib -source: - sha256: c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 - url: http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2 - test: commands: - "samtools view --help 2>&1 | grep Notes > /dev/null" +about: + home: https://github.com/samtools/samtools + license: MIT + summary: Tools for dealing with SAM, BAM and CRAM files + extra: identifiers: - biotools:samtools