diff --git a/recipes/perl-bio-searchio-hmmer/build.sh b/recipes/perl-bio-searchio-hmmer/build.sh new file mode 100644 index 0000000000000..13104878add47 --- /dev/null +++ b/recipes/perl-bio-searchio-hmmer/build.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +set -o errexit -o pipefail + +# If it has Build.PL use that, otherwise use Makefile.PL +if [[ -f Build.PL ]]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./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 +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-bio-searchio-hmmer/meta.yaml b/recipes/perl-bio-searchio-hmmer/meta.yaml new file mode 100644 index 0000000000000..a9932e8254d76 --- /dev/null +++ b/recipes/perl-bio-searchio-hmmer/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "perl-bio-searchio-hmmer" %} +{% set version = "1.7.3" %} +{% set sha256 = "686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/Bio-SearchIO-hmmer-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: generic + number: 0 + run_exports: + weak: + - {{ name }} ={{ version }} + +requirements: + build: + - make + host: + - perl + - perl-bioperl-core + - perl-io-string + - perl-test-most + - perl-db_file + run: + - perl + - perl-bioperl-core + - perl-io-string + - perl-db_file + +test: + imports: + - Bio::Index::Hmmer + - Bio::Search::HSP::HMMERHSP + - Bio::Search::HSP::HmmpfamHSP + - Bio::Search::Hit::HMMERHit + - Bio::Search::Hit::HmmpfamHit + - Bio::Search::Hit::hmmer3Hit + - Bio::Search::Result::HMMERResult + - Bio::Search::Result::HmmpfamResult + - Bio::Search::Result::hmmer3Result + - Bio::SearchIO::hmmer + - Bio::SearchIO::hmmer2 + - Bio::SearchIO::hmmer3 + - Bio::SearchIO::hmmer_pull + - Bio::Tools::HMMER::Domain + - Bio::Tools::HMMER::Results + - Bio::Tools::HMMER::Set + - Bio::Tools::Hmmpfam + +about: + home: https://metacpan.org/release/Bio-SearchIO-hmmer + license: perl_5 + summary: 'A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)' diff --git a/recipes/perl-bioperl-core/meta.yaml b/recipes/perl-bioperl-core/meta.yaml index 81090d5c59bbd..912086ea9a14e 100644 --- a/recipes/perl-bioperl-core/meta.yaml +++ b/recipes/perl-bioperl-core/meta.yaml @@ -13,7 +13,8 @@ source: # 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. build: - number: 0 + noarch: generic + number: 1 run_exports: weak: - {{ name }} ={{ version }} @@ -42,10 +43,12 @@ requirements: - perl-yaml - perl-xml-twig # Required at least for testing + # (run-time dependency for Bio::Index and its descendants) - perl-db_file run: - perl + - perl-db_file #- perl-xml-writer #- perl-uri #- perl-xml-dom diff --git a/recipes/perl-bioperl/meta.yaml b/recipes/perl-bioperl/meta.yaml index fba47e8a3a2e7..e2259b4ab9e90 100644 --- a/recipes/perl-bioperl/meta.yaml +++ b/recipes/perl-bioperl/meta.yaml @@ -5,13 +5,20 @@ package: build: noarch: generic - number: 0 + number: 1 + +# no tests because this is a metapackage, +# but satisfy the linter. +test: + commands: + - echo "foo" requirements: run: - perl - perl-bioperl-core {{ version }} - perl-bioperl-run + - perl-bio-searchio-hmmer - perl-bio-tools-phylo-paml - perl-bio-tools-run-alignment-tcoffee # [linux] - perl-bio-tools-run-alignment-clustalw diff --git a/recipes/prokka/meta.yaml b/recipes/prokka/meta.yaml index aab6a920626a3..989ccee2c6188 100644 --- a/recipes/prokka/meta.yaml +++ b/recipes/prokka/meta.yaml @@ -11,19 +11,19 @@ source: sha256: '{{ sha256 }}' build: - number: 3 + number: 4 noarch: generic requirements: host: - - perl 5.26.2 - - perl-bioperl 1.7.2 + - perl + - perl-bioperl >=1.7.2 - perl-xml-simple - blast >=2.7.1 - infernal >=1.1.2 - hmmer >=3.1b2 run: - - perl 5.26.2 + - perl - aragorn >=1.2 - barrnap >=0.7 - blast >=2.7.1 @@ -31,7 +31,7 @@ requirements: - infernal >=1.1.2 - minced >=0.3 - parallel >=20180522 - - perl-bioperl 1.7.2 + - perl-bioperl >=1.7.2 - perl-xml-simple - prodigal >=2.6 - tbl2asn-forever >=25.7