Convert Travis CI to Github Actions (#662)

* convert travisci to gha

* tweak reccipe

* add dependency

* fix typo

* oh tbl2asn

* more tbl2asn complications

* almost there with tbl2asn

* tbl2asn not going down without a fight

* typos

* cleanup tbl2asn

* tbl2asn

* tbl2asn

* typo

* install depends with conda

* fix bash entry

Author: rpetit3

.github/workflows/test-prokka.yml

@@ -0,0 +1,40 @@
+name: Prokka Tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Pull Prokka
+        uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.10'
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          channel-priority: strict
+          activate-environment: prokka
+          environment-file: environment.yml
+          auto-update-conda: true
+
+      - name: Add Prokka to PATH
+        run: |
+          rm -rf "${{ github.workspace }}/binaries"
+          echo "${{ github.workspace }}/bin" >> $GITHUB_PATH
+
+      - name: Test Prokka
+        run: |
+          prokka --version
+          prokka --help
+          ! prokka --doesnotexist
+          prokka --depends
+          prokka --setupdb
+          prokka --listdb
+          prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna
+          grep '>' asm/asm.fna
+          prokka --cleandb

.travis.yml

@@ -0,0 +1,16 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - 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-xml-simple
+  - prodigal >=2.6
+  - tbl2asn-forever >=25.7