more from bioconda#15196 (bioconda#15326)

* more from bioconda#15196

* bump build numbers

* updates

* updates

* old bedtools versions won't build, fix bcftools/1.3.1

* group blacklist items a bit

* Try to fix braker and bowtie2

* a few updates

* Update meta.yaml

build-fail-blacklist

@@ -1,3 +1,7 @@
+# ../../utils//fileType/FileRecordTypeChecker.h:120:21: error: 'constexpr' needed for in-class initialization of static data member 'const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE' of non-integral type [-fpermissive]
+recipes/bedtools/2.20.1
+recipes/bedtools/2.19.1
+
 # last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
 recipes/last/638
 
@@ -168,6 +172,14 @@ recipes/soapaligner
 # missing tarball
 recipes/metagene_annotator
 recipes/sloika
+recipes/genometools
+recipes/nanonet
+recipes/knot
+recipes/moreutils
+recipes/jali
+recipes/intervalstats
+recipes/mrbayes
+recipes/igvtools
 
 # missing dep
 recipes/oligotyping
@@ -209,6 +221,7 @@ recipes/libmuscle
 
 # compilation error
 recipes/osra/2.0.1
+recipes/lightning
 
 # unable to access jarfile
 recipes/effectivet3
@@ -222,9 +235,6 @@ recipes/discovar-denovo
 # seqan errors
 recipes/bowtie/1.0.0
 
-# tarball missing
-recipes/mrbayes
-
 # depends on perl-pcap
 recipes/brass
 
@@ -243,10 +253,6 @@ recipes/qiime/1.9.1
 # requires wgs-assembler, which has a build fail
 recipes/sprai
 
-# missing tarballs
-recipes/genometools
-recipes/nanonet
-
 # missing dependency
 recipes/genomebaser
 recipes/garnet
@@ -329,9 +335,6 @@ recipes/primerprospector
 # missing URL
 recipes/intemap
 
-# compilation error
-recipes/lightning
-
 # zlib missing
 recipes/polymutt
 recipes/prophyle/0.2.1
@@ -504,9 +507,6 @@ recipes/perl-bio-db-sam
 recipes/krona/2.6
 recipes/krona/2.5
 
-# tarball missing
-recipes/igvtools
-
 # /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)
 recipes/pash
 
@@ -546,17 +546,9 @@ recipes/ghc/6.8.3
 # missing python dep
 recipes/hurry.filesize
 
-# missing tarball
-recipes/knot
-recipes/moreutils
-
 # compilation error, missing boost header
 recipes/k-slam
 
-# missing tarball
-recipes/jali
-recipes/intervalstats
-
 # failing
 recipes/igblast/1.4.0
 
@@ -732,7 +724,6 @@ recipes/bioconductor-org.mm.eg.db/3.3.0
 recipes/bioconductor-qdnaseq.mm10/1.4.0
 recipes/bioconductor-rgraphviz/2.13.0
 recipes/bioconductor-ropls/1.2.14
-recipes/r-seurat/1.4.0.16
 recipes/r-speaq/1.2.1
 recipes/bioconductor-cummerbund/2.8.2
 recipes/bioconductor-cummerbund/2.12.1

recipes/bcftools/1.3.1/build.sh

@@ -2,4 +2,5 @@
 
 export CPPFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
-make prefix=$PREFIX CPPFLAGS=$CPPFLAGS LDFLAGS=$LDFLAGS plugins install
+make all prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS"
+make install prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS"

recipes/bcftools/1.3.1/meta.yaml

@@ -1,20 +1,14 @@
-about:
-  home: https://github.com/samtools/bcftools
-  license: MIT
-  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
-    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
-    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
-    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
-    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
-    VCF and BCF and streams will work in most, but not all situations.
-
-build:
-  number: 4
-
 package:
   name: bcftools
   version: '1.3.1'
 
+source:
+  sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924
+  url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
+
+build:
+  number: 5
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -23,16 +17,23 @@ requirements:
   run:
     - zlib
 
-source:
-  sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924
-  url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
-
 test:
   commands:
     - "bcftools -h > /dev/null"
     - bcftools --version
     - bcftools plugin -lv
 
+about:
+  home: https://github.com/samtools/bcftools
+  license: MIT
+  license_file: "LICENSE"
+  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
+    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
+    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
+    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
+    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
+    VCF and BCF and streams will work in most, but not all situations.
+
 extra:
   identifiers:
     - biotools:bcftools

recipes/bcftools/meta.yaml

@@ -1,19 +1,16 @@
 {% set version="1.9" %}
-about:
-  home: https://github.com/samtools/bcftools
-  license: MIT
-  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
-    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
-    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
-    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
-    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
-    VCF and BCF and streams will work in most, but not all situations.
 
-build:
-  number: 3
 package:
   name: bcftools
   version: {{ version }}
+
+build:
+  number: 4
+
+source:
+  url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2
+  sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -33,17 +30,23 @@ requirements:
     - zlib
     - libdeflate
 
-source:
-  url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2
-  sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8
-
 test:
   commands:
     - bcftools -h
     - bcftools --version
     - bcftools plugin -lv
     #- plot-vcfstats -h 2>&1 | grep -q "Plots output of "
 
+about:
+  home: https://github.com/samtools/bcftools
+  license: MIT
+  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
+    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
+    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
+    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
+    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
+    VCF and BCF and streams will work in most, but not all situations.
+
 extra:
   identifiers:
     - biotools:bcftools

recipes/bedtools/2.19.1/build.sh

@@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make
+make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib"
 mkdir -p $PREFIX/bin
 mv bin/* $PREFIX/bin/

recipes/bedtools/2.19.1/meta.yaml

@@ -1,31 +1,32 @@
-about:
-  home: http://bedtools.readthedocs.org/
-  license: GPL v2
-  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
-
-build:
-  number: 2
-
 package:
   name: bedtools
   version: 2.19.1
 
+source:
+  sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77
+  url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz
+
+build:
+  number: 3
+
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - zlib
   run:
     - zlib
 
-source:
-  sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77
-  url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz
-
 test:
   commands:
     - bedtools
 
+about:
+  home: http://bedtools.readthedocs.org/
+  license: GPL v2
+  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
+
 extra:
   identifiers:
     - biotools:bedtools

recipes/bedtools/2.20.1/build.sh

@@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make
-mkdir -p $PREFIX/bin
-mv bin/* $PREFIX/bin/
+make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib"
+mkdir -p ${PREFIX}/bin
+mv bin/* ${PREFIX}/bin/

recipes/bedtools/2.20.1/meta.yaml

@@ -1,31 +1,32 @@
-about:
-  home: http://bedtools.readthedocs.org/
-  license: GPL v2
-  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
-
-build:
-  number: 2
-
 package:
   name: bedtools
   version: 2.20.1
 
+source:
+  sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3
+  url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz
+
+build:
+  number: 3
+
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - zlib
   run:
     - zlib
 
-source:
-  sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3
-  url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz
-
 test:
   commands:
     - bedtools
 
+about:
+  home: http://bedtools.readthedocs.org/
+  license: GPL v2
+  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
+
 extra:
   identifiers:
     - biotools:bedtools

recipes/bedtools/2.22/build.sh

@@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make install prefix=$PREFIX
+make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib"

recipes/bedtools/2.22/meta.yaml

@@ -1,31 +1,33 @@
-about:
-  home: http://bedtools.readthedocs.org/
-  license: GPL v2
-  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
-
-build:
-  number: 2
-
 package:
   name: bedtools
   version: '2.22'
 
+source:
+  sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233
+  url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz
+
+build:
+  number: 3
+  skip: True  # [osx]
+
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - zlib
   run:
     - zlib
 
-source:
-  sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233
-  url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz
-
 test:
   commands:
     - bedtools
 
+about:
+  home: http://bedtools.readthedocs.org/
+  license: GPL v2
+  summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
+
 extra:
   identifiers:
     - biotools:bedtools

recipes/bedtools/2.23.0/build.sh

@@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make install prefix=$PREFIX
+make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib"