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* 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
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dpryan79 authored and kpalin committed Aug 7, 2019
1 parent f5c20ad commit 2f97adb
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Showing 19 changed files with 168 additions and 166 deletions.
35 changes: 13 additions & 22 deletions build-fail-blacklist
Original file line number Diff line number Diff line change
@@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -209,6 +221,7 @@ recipes/libmuscle

# compilation error
recipes/osra/2.0.1
recipes/lightning

# unable to access jarfile
recipes/effectivet3
Expand All @@ -222,9 +235,6 @@ recipes/discovar-denovo
# seqan errors
recipes/bowtie/1.0.0

# tarball missing
recipes/mrbayes

# depends on perl-pcap
recipes/brass

Expand All @@ -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
Expand Down Expand Up @@ -329,9 +335,6 @@ recipes/primerprospector
# missing URL
recipes/intemap

# compilation error
recipes/lightning

# zlib missing
recipes/polymutt
recipes/prophyle/0.2.1
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion recipes/bcftools/1.3.1/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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"
35 changes: 18 additions & 17 deletions recipes/bcftools/1.3.1/meta.yaml
Original file line number Diff line number Diff line change
@@ -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') }}
Expand All @@ -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
Expand Down
33 changes: 18 additions & 15 deletions recipes/bcftools/meta.yaml
Original file line number Diff line number Diff line change
@@ -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') }}
Expand All @@ -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
Expand Down
2 changes: 1 addition & 1 deletion recipes/bedtools/2.19.1/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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/
25 changes: 13 additions & 12 deletions recipes/bedtools/2.19.1/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
6 changes: 3 additions & 3 deletions recipes/bedtools/2.20.1/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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/
25 changes: 13 additions & 12 deletions recipes/bedtools/2.20.1/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
2 changes: 1 addition & 1 deletion recipes/bedtools/2.22/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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"
26 changes: 14 additions & 12 deletions recipes/bedtools/2.22/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
2 changes: 1 addition & 1 deletion recipes/bedtools/2.23.0/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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"

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