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abretaudabretaud
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Unblacklist 3 perl modules (#13713)
* unblacklist 3 perl modules * trying to fix building * merge * need gcc * dep * fix test * wrong package name? * skip tests as they are very basic + need a specific module * add missing module * add dep * revert unneeded change * relax constraints * add missing deps * fix cpanm error on osx
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lines changed

23 files changed

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‎build-fail-blacklist‎

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@@ -248,9 +248,6 @@ recipes/qiime/1.9.1
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# requires wgs-assembler, which has a build fail
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recipes/sprai
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# missing perl dep
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recipes/perl-text-ansitable/0.48
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# missing tarballs
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recipes/genometools
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recipes/nanonet
@@ -530,7 +527,6 @@ recipes/perl-module-fromperlver/0.008002
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# test failed:
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recipes/perl-locale-maketext-simple/0.21
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recipes/perl-mldbm-sync
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recipes/perl-pod-checker/1.60
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# /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)
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recipes/pash
@@ -611,9 +607,7 @@ recipes/ra-integrate
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# Unknown issues
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recipes/perl-pcap
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recipes/perl-hpc-runner-command/3.2.13
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recipes/perl-biox-workflow-command
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recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3
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# real long build-time
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recipes/perl-bio-viennangs

‎recipes/perl-archive-tar-wrapper/0.33/build.sh‎

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

‎recipes/perl-archive-tar-wrapper/0.33/meta.yaml‎

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{% set name = "perl-archive-tar-wrapper" %}
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{% set version = "0.33" %}
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{% set sha256 = "8afd18e41a9274d897f7b70db44a32eac012eb3be74d5e378c967042df7ed67c" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://cpan.metacpan.org/authors/id/A/AR/ARFREITAS/Archive-Tar-Wrapper-0.33.tar.gz
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sha256: {{ sha256 }}
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build:
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number: 0
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requirements:
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build:
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- perl
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- perl-file-temp
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- perl-extutils-makemaker
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- perl-file-which
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- perl-test-simple
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- perl-log-log4perl
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- perl-ipc-run
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- perl-dumbbench
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run:
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- perl
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- perl-file-which
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- perl-ipc-run
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- perl-log-log4perl
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- perl-file-temp
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test:
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imports:
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- Archive::Tar::Wrapper
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about:
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home: http://metacpan.org/pod/Archive::Tar::Wrapper
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license: gpl_3
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summary: "API wrapper around the 'tar' utility"

‎recipes/perl-biosails/0.02/build.sh‎

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#!/bin/bash
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# If it has Build.PL use that, otherwise use Makefile.PL
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if [ -f Build.PL ]; then
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perl Build.PL
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perl ./Build
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# Make sure this goes in site
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perl ./Build install --installdirs site
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elif [ -f Makefile.PL ]; then
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# Make sure this goes in site
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perl Makefile.PL INSTALLDIRS=site
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make
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make install
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else
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echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
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exit 1
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fi

‎recipes/perl-biosails/0.02/meta.yaml‎

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{% set name = "perl-biosails" %}
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{% set version = "0.02" %}
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{% set sha256 = "7f700086f2c66ecefba0c306aacd7615cbfeb7df3995b30808148484af69c9f5" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://cpan.metacpan.org/authors/id/J/JI/JILLROWE/BioSAILs-0.02.tar.gz
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sha256: {{ sha256 }}
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build:
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number: 0
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requirements:
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build:
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- perl
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- perl-namespace-autoclean
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- perl-moosex-types-path-tiny
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- perl-path-tiny
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- perl-data-dumper
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- perl-git-wrapper
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- perl-moosex-types
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- perl-ipc-cmd
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- perl-hash-merge
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- perl-capture-tiny
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- perl-file-temp
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- perl-sort-versions
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- perl-version-next
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- perl-file-path
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- perl-file-slurp
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- perl-config-any
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- perl-yaml
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- perl-datetime
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- perl-moose
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- perl-moosex-object-pluggable
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- perl-module-build-tiny
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- perl-test-class-moose
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- perl-try-tiny
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- perl-file-homedir
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- perl-moosex-app
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run:
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- perl
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- perl-sort-versions
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- perl-namespace-autoclean
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- perl-moosex-types-path-tiny
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- perl-path-tiny
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- perl-data-dumper
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- perl-git-wrapper
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- perl-git-wrapper-plus
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- perl-file-slurp
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- perl-config-any
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- perl-moosex-types
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- perl-yaml
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- perl-ipc-cmd
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- perl-datetime
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- perl-hash-merge
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- perl-moosex-object-pluggable
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- perl-file-path
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- perl-try-tiny
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- perl-capture-tiny
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- perl-file-homedir
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- perl-version-next
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- perl-file-temp
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- perl-moosex-app
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test:
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imports:
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- BioSAILs
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- BioSAILs::Integrations::Github
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- BioSAILs::Utils
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- BioSAILs::Utils::CacheUtils
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- BioSAILs::Utils::Files::CacheDir
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- BioSAILs::Utils::LoadConfigs
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- BioSAILs::Utils::Plugin
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- BioSAILs::Utils::Traits
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about:
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home: https://github.com/biosails/BioSAILs
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license: perl_5
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summary: 'Standard(ized) Analysis Information Layers'

‎recipes/perl-devel-checkos/1.81/build.sh‎

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#!/bin/bash
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# If it has Build.PL use that, otherwise use Makefile.PL
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if [ -f Build.PL ]; then
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perl Build.PL
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perl ./Build
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perl ./Build test
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# Make sure this goes in site
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perl ./Build install --installdirs site
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elif [ -f Makefile.PL ]; then
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# Make sure this goes in site
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perl Makefile.PL INSTALLDIRS=site
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make
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make test
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make install
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else
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echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
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exit 1
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fi

‎recipes/perl-devel-checkos/1.81/meta.yaml‎

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{% set name = "perl-devel-checkos" %}
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{% set version = "1.81" %}
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{% set sha256 = "f3c17b56b79283b62616f938d36c57adc9df06bfaa295ff98be21e9014a23b10" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL/Devel-CheckOS-1.81.tar.gz
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sha256: {{ sha256 }}
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build:
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number: 0
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requirements:
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build:
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- perl
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- perl-extutils-makemaker
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- perl-file-temp
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- perl-data-compare
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- perl-file-find-rule
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run:
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- perl
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- perl-file-temp
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- perl-file-find-rule
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- perl-data-compare
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test:
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imports:
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- Devel::CheckOS
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about:
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home: http://metacpan.org/pod/Devel::CheckOS
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license: unknown
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summary: "check what OS we're running on"

‎recipes/perl-dumbbench/0.111/build.sh‎

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#!/bin/bash
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# If it has Build.PL use that, otherwise use Makefile.PL
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if [ -f Build.PL ]; then
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perl Build.PL
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perl ./Build
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perl ./Build test
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# Make sure this goes in site
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perl ./Build install --installdirs site
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elif [ -f Makefile.PL ]; then
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# Make sure this goes in site
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perl Makefile.PL INSTALLDIRS=site
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make
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make test
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make install
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else
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echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
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exit 1
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fi

‎recipes/perl-dumbbench/0.111/meta.yaml‎

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{% set name = "perl-dumbbench" %}
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{% set version = "0.111" %}
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{% set sha256 = "d31d3ca7d672bd928183ccbf29d3275ea594f7d324ae5f49db6182967c5ab2c7" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://cpan.metacpan.org/authors/id/B/BD/BDFOY/Dumbbench-0.111.tar.gz
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sha256: {{ sha256 }}
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build:
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number: 0
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requirements:
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build:
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- perl
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- perl-carp
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- perl-parent
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- perl-capture-tiny
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- perl-time-hires
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- perl-extutils-makemaker
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- perl-params-util
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- perl-class-xsaccessor
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- perl-devel-checkos
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- perl-number-witherror
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- perl-statistics-caseresampling
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run:
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- perl
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- perl-carp
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- perl-parent
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- perl-capture-tiny
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- perl-time-hires
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- perl-params-util
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- perl-statistics-caseresampling
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- perl-class-xsaccessor
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- perl-devel-checkos
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- perl-number-witherror
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test:
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imports:
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- Dumbbench
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about:
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home: https://github.com/briandfoy/dumbbench
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license: perl_5
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summary: 'More reliable benchmarking with the least amount of thinking'

‎recipes/perl-hpc-runner-command/3.2.13/meta.yaml‎

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@@ -53,7 +53,6 @@ requirements:
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- perl-text-asciitable
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- perl-try-tiny
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- perl-json
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- perl-datetime
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- perl-test-class-moose
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- perl-path-tiny
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- perl-template-toolkit
@@ -66,6 +65,10 @@ requirements:
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- perl-types-standard
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- perl-number-compare
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- perl-file-find-rule
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- perl-archive-tar-wrapper
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- perl-biosails
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- perl-data-uuid
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- perl-slurp
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run:
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- perl
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- perl-namespace-autoclean
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- perl-io-interactive # [linux]
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- perl-list-uniq
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- perl-datetime
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- perl-text-asciitable
102104
- perl-try-tiny
103105
- perl-json
@@ -113,6 +115,10 @@ requirements:
113115
- perl-number-compare
114116
- perl-file-find-rule
115117
- perl-list-moreutils >=0.428
118+
- perl-archive-tar-wrapper
119+
- perl-biosails
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- perl-data-uuid
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- perl-slurp
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test:
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commands:
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home: https://github.com/biosails/HPC-Runner-Command
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license: perl_5
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summary: 'Create composable bioinformatics hpc analyses.'
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