[ci skip] Merge PR 33805

Merge PR #33805, commits were: 
 * Update meta.yaml
 * perl-bioperl: make test-command a string

I meant to use the program 'true', but yaml interpreted it as a bool
without the quotes.
 * Avoid the solver giving broken dependencies.
 * Merge remote-tracking branch 'upstream/master' into perl-bio-searchio-hmmer
 * perl-bioperl{,-core}: clean up pre-existing lint
 * prokka: remove pinning of perl and bioperl versions

Now that Bio::SearchIO::hmmer is packaged, we can use it as part
of the latest bioperl distribution and there's no longer a need
for this pinning.

This reverts the workaround a32603c
in favor of resolving the underlying problem.
 * Add perl-bio-searchio-hmmer

This module was split out of the main bioperl distribution in
version 1.7.3 (https://metacpan.org/dist/BioPerl/changes), but
is still needed by Prokka (#33356).
 * perl-bioperl-core: add run-time depends on perl-db_file

This is needed for Bio::Index objects and classes that descend
from it for the creation of index files.

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.

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)'

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

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

recipes/prokka/meta.yaml

@@ -11,27 +11,27 @@ 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
     - hmmer >=3.1b2
     - 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