Merge pull request #3 from bioconda/master

merge with bioconda master

.travis.yml

@@ -11,7 +11,7 @@ env:
   global:
   - secure: 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
   - SUBDAGS=2
-  - BIOCONDA_UTILS_TAG=4d8ddcd8718b77cec8aaa216f02acfaeb9b663c3
+  - BIOCONDA_UTILS_TAG=9b7ab8070f9be300a533c702a843b3fb1d613b8c
   - BIOCONDA_UTILS_ARGS="--loglevel=info --mulled-test"
   matrix:
   - SUBDAG=0

build-fail-blacklist

@@ -1,6 +1 @@
-<<<<<<< 66e5051fa837e9c54553b8eeb46fe67d93d5b18b
-#recipes/autoconf
-=======
-recipes/autoconf
-recipes/msproteomicstools
->>>>>>> blacklist msproteomicstools
+ recipes/vsearch

recipes/bumbershoot/meta.yaml

@@ -0,0 +1,34 @@
+{% set version = "3_0_10158" %}
+{% set root = "pwiz_tools/Bumbershoot/" %}
+{% set targets = root~"myrimatch//install "~root~"directag//install "~root~"tagrecon//install "~root~"idpicker//install "~root~"pepitome//install "~root~"quameter//install" %}
+
+package:
+  name: bumbershoot
+  version: {{ version }}
+
+source:
+  url: http://teamcity.labkey.org/guestAuth/repository/download/BumbershootSubsetSourceTarball/380430:id/bumbershoot-src-without-t-{{ version }}.tar.bz2
+  sha1: 28cd2a1d49e735a631f9315e23b076371e5fb11e
+
+build:
+  script: bash -c "./quickbuild.sh -j{{ CPU_COUNT }} address-model=64 runtime-link=shared {{ targets }} && cp build-linux-x86_64/gcc-release-x86_64/* $PREFIX/bin"
+  skip: True # [osx]
+
+requirements:
+  build:
+    - gcc   # [linux]
+  run:
+    - libgcc # [linux]
+
+
+about:
+  home: https://proteowizard.sourceforge.net
+  license: Apache 2.0
+  summary: The Bumbershoot tool suite for analyzing shotgun proteomic data
+
+test:
+  commands:
+    - myrimatch --help
+    - directag --help
+    - quameter --help
+    - pepitome --help

recipes/geneimpacts/meta.yaml

@@ -1,12 +1,11 @@
 package:
   name: geneimpacts
-  version: '0.1.4'
+  version: '0.2.0'
 
 source:
-  fn: geneimpacts-de9be10.tar.gz
-  url: https://github.com/brentp/geneimpacts/archive/de9be10.tar.gz
-  #url: https://pypi.python.org/packages/dc/19/c8e9c9c0eddad996992b78640d9afe8ff459d7ee992d54ce3be9023e807f/geneimpacts-0.1.3.tar.gz
-  #md5: 764ecf6a30bd720911700bc5a6aa06bf
+  fn: geneimpacts-0.2.0.tar.gz
+  url: https://pypi.python.org/packages/c8/00/d1d713a340e7bea720d09202c5f0a5b5744fd8e10b7451462887b48d4f7e/geneimpacts-0.2.0.tar.gz
+  md5: 49b1505e4946336ee399d6bd2ebf2b17
 
 build:
   number: 1

recipes/jbrowse/build.sh

@@ -11,9 +11,10 @@ chmod a+x $PREFIX/etc/conda/deactivate.d/jbrowse-sourcedir.sh
 cd $SRC_DIR
 
 mkdir -p $PREFIX/bin/
-cp bin/* $PREFIX/bin/
-chmod a+x $PREFIX/bin/*
-sed -i.bak 's|../src/perl5|../opt/jbrowse/src/perl5|g' $PREFIX/bin/*
+cp bin/*.pl $PREFIX/bin/
+chmod a+x $PREFIX/bin/*.pl
+sed -i.bak 's|../src/perl5|../opt/jbrowse/src/perl5|g' $PREFIX/bin/*.pl
+rm $PREFIX/bin/*.pl.bak
 
 mkdir -p $PREFIX/opt/jbrowse/
 cp -r * $PREFIX/opt/jbrowse/

recipes/jbrowse/meta.yaml

@@ -2,7 +2,7 @@ package:
   name: jbrowse
   version: "1.12.1"
 build:
-  number: 1
+  number: 2
   skip: True # [osx]
 source:
   fn: jbrowse-1.12.1.zip

recipes/multiqc-bcbio/meta.yaml

@@ -1,13 +1,13 @@
 package:
   name: multiqc-bcbio
-  version: "0.1.7"
+  version: "0.1.8"
 
 source:
   git_url: https://github.com/lpantano/MultiQC_bcbio
-  git_tag: 49b1f8b41def201f5cd18c92ab0332d8b8775785
+  git_tag: 393a91ae70690f83cd781b64e101e66b803723d0
 
 build:
-  number: 1
+  number: 0
   preserve_egg_dir: True
   skip: False
 

recipes/percolator/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+mkdir percobuild && cd percobuild
+cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" $SRC_DIR
+make && make install
+cd ..
+
+mkdir converterbuild && cd converterbuild 
+cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DBOOST_ROOT=$PREFIX -DBOOST_LIBRARYDIR=$PREFIX/lib -DSERIALIZE="TokyoCabinet" -DCMAKE_PREFIX_PATH=$PREFIX $SRC_DIR/src/converters
+make && make install

recipes/percolator/meta.yaml

@@ -0,0 +1,45 @@
+package:
+  name: percolator
+  version: '3.0'
+
+source:
+  fn: rel-3-00.tar.gz
+  url: https://github.com/percolator/percolator/archive/rel-3-00.tar.gz
+  md5: de87c96643fed652e454ac492ce850b4
+
+build:
+  number: 0
+  string: boost_1.62_{{PKG_BUILDNUM}}
+  skip: True # [osx]
+
+requirements:
+  build:
+    - cmake ==2.8.10.2
+    - gcc
+    - zlib
+    - boost ==1.62
+    - tokyocabinet
+    - sqlite
+    - bzip2
+    - xerces-c ==3.1.2
+    - xsd
+  run:
+    - gcc
+    - zlib
+    - boost ==1.62
+    - tokyocabinet
+    - sqlite
+    - bzip2
+    - xerces-c ==3.1.2
+    - xsd
+
+
+test:
+  commands:
+    - percolator --help 2>&1 > /dev/null | grep "Percolator version 3.00"
+    - msgf2pin --help
+
+about:
+  home: https://github.com/percolator/percolator
+  license: Apache 2.0
+  summary: Semi-supervised learning for peptide identification from shotgun proteomics datasets

recipes/perl-apache-test/build.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# If it has Build.PL use that, otherwise use Makefile.PL
+if [ -f Build.PL ]; then
+    perl Build.PL
+    ./Build
+    ./Build test
+    # Make sure this goes in site
+    ./Build install --installdirs site
+elif [ -f Makefile.PL ]; then
+    # Make sure this goes in site
+    perl Makefile.PL INSTALLDIRS=site
+    make
+    make test
+    make install
+else
+    echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
+    exit 1
+fi
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

recipes/perl-apache-test/meta.yaml

@@ -0,0 +1,47 @@
+package:
+  name: perl-apache-test
+  version: "1.40"
+
+source:
+  fn: Apache-Test-1.40.tar.gz
+  url: https://cpan.metacpan.org/authors/id/S/SH/SHAY/Apache-Test-1.40.tar.gz
+  md5: 78e059bccfa0c2f0297ff2fca591eca9
+#  patches:
+   # List any patch files here
+   # - fix.patch
+
+# build:
+  # If this is a new build for the same version, increment the build
+  # number. If you do not include this key, it defaults to 0.
+  # number: 1
+
+requirements:
+  build:
+    - perl-threaded
+    - perl-pathtools
+    - perl-extutils-makemaker
+
+  run:
+    - perl-threaded
+    - perl-pathtools
+
+test:
+  # Perl 'use' tests
+  imports:
+    - Apache::Test
+
+  # You can also put a file called run_test.pl (or run_test.py) in the recipe
+  # that will be run at test time.
+
+  # requires:
+    # Put any additional test requirements here.  For example
+    # - nose
+
+about:
+  home: http://metacpan.org/pod/Apache::Test
+  license: unknown
+  summary: 'Special Tests Sequence Failure Finder'
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml

recipes/perl-archive-tar/build.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# If it has Build.PL use that, otherwise use Makefile.PL
+if [ -f Build.PL ]; then
+    perl Build.PL
+    ./Build
+    #./Build test
+    # Make sure this goes in site
+    ./Build install --installdirs site
+elif [ -f Makefile.PL ]; then
+    # Make sure this goes in site
+    perl Makefile.PL INSTALLDIRS=site
+    make
+    #make test
+    make install
+else
+    echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
+    exit 1
+fi
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

recipes/perl-archive-tar/meta.yaml

@@ -0,0 +1,36 @@
+package:
+  name: perl-archive-tar
+  version: 2.18
+
+source:
+  fn: Archive-Tar-2.18.tar.gz
+  url: http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/Archive-Tar-2.18.tar.gz
+  md5: ed4d4ca0124adece439f5d97b05d3987
+
+build:
+  number: 1
+
+requirements:
+  build:
+    - perl-threaded
+    - perl-pathtools
+    - perl-io-compress
+    - perl-io-zlib
+    - perl-test-harness
+    - perl-test-simple
+
+  run:
+
+test:
+  # Perl 'use' tests
+  imports:
+    - Archive::Tar
+    - Archive::Tar::Constant
+    - Archive::Tar::File
+
+
+about:
+  home: http://metacpan.org/pod/Archive::Tar
+  license: perl_5
+  summary: 'Manipulates TAR archives'
+

recipes/perl-class-accessor/build.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# If it has Build.PL use that, otherwise use Makefile.PL
+if [ -f Build.PL ]; then
+    perl Build.PL
+    ./Build
+    ./Build test
+    # Make sure this goes in site
+    ./Build install --installdirs site
+elif [ -f Makefile.PL ]; then
+    # Make sure this goes in site
+    perl Makefile.PL INSTALLDIRS=site
+    make
+    make test
+    make install
+else
+    echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
+    exit 1
+fi
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.