[ci skip] Merge PR 34517

Merge PR bioconda#34517, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add new package mgca * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local
nextstrain · Apr 26, 2022 · a256f17 · a256f17
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diff --git a/recipes/mgca/build.sh b/recipes/mgca/build.sh
@@ -0,0 +1,27 @@
+#!/bin/sh
+mkdir -p $PREFIX/bin
+
+cp mgca.pl $PREFIX/bin/mgca
+cp Scripts/setupDB.pl $PREFIX/bin/setupDB
+cp Scripts/pI/print_pI.pl $PREFIX/bin/
+cp Scripts/pI/plot_pI.R $PREFIX/bin/
+cp Scripts/IS/run_islandpath.pl $PREFIX/bin/
+cp Scripts/PROPHAGE/run_PhiSpy.pl $PREFIX/bin/
+cp Scripts/CRISPR/run_opfi.py $PREFIX/bin/
+cp Scripts/CRISPR/db/cas_all_* $PREFIX/bin/
+cp Scripts/CRISPR/db/cas1_db.* $PREFIX/bin/
+
+
+chmod a+x $PREFIX/bin/mgca
+chmod a+x $PREFIX/bin/setupDB
+chmod a+x $PREFIX/bin/print_pI.pl
+chmod a+x $PREFIX/bin/plot_pI.R
+chmod a+x $PREFIX/bin/run_islandpath.pl
+chmod a+x $PREFIX/bin/run_PhiSpy.pl
+chmod a+x $PREFIX/bin/run_opfi.py
+chmod a+x $PREFIX/bin/cas_all_*
+chmod a+x $PREFIX/bin/cas1_db.*
+
+
+mgca --version
+mgca --help
diff --git a/recipes/mgca/meta.yaml b/recipes/mgca/meta.yaml
@@ -0,0 +1,66 @@
+{% set name = "mgca" %}
+{% set version = "0.0.0" %}
+
+package:
+  name: '{{ name }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/liaochenlanruo/mgca/archive/v{{ version }}.tar.gz
+  sha256: 219e4fafe180a25c29c665f43ea0eccbcfbffa49ea5db22929ea9c9828a747c0
+
+
+build:
+  number: 0
+  noarch: generic
+
+requirements:
+  host:
+    - perl
+  run:
+    - perl
+    ##- prokka
+    - perl-bioperl
+    - emboss
+    #- gtdbtk
+    - islandpath 1.0.6
+    - phispy 4.2.21
+    - opfi 0.1.2
+    ##- trnascan-se
+    #- infernal 1.1.4
+    #- bakta 1.4.0
+    ##- trf
+    #- repeatmasker 4.1.2.p1
+    #- mummer4 4.0.0rc1
+    #- artemis 18.2.0
+    #- saspector 0.0.5
+    #- lastz 1.04.15
+    #- kakscalculator2
+    #- interproscan 5.54_87.0
+    #- eggnog-mapper 2.1.7
+    - r-ggplot2
+    - wget
+    ##- openjdk
+
+test:
+  commands:
+    - mgca --version
+    - mgca --help
+
+about:
+  home: https://github.com/liaochenlanruo/mgca/blob/master/README.md
+  license: GPLv3
+  license_family: GPL
+  license_file: LICENSE
+  summary: Microbial genome component and annotation pipeline
+  description: Microbial genome component and annotation pipeline.
+  dev_url: https://github.com/liaochenlanruo/mgca/tree/master
+  doc_url: https://liaochenlanruo.fun/mgca/
+
+extra:
+  identifiers:
+    - biotools:mgca
+  recipe-maintainers:
+    - liaochenlanruo
+  doi:
+    - NA