Update to 20.05

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: Test Docker image building
+
+on: [push, pull_request]
+env:
+  TOX_ENV: py37
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install test script
+        run: |
+          wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
+          # As Test VM disk space is limited, we remove all conda envs once they are installed successfully to free some disk space (see #23)
+          sed -i 's|\(install-tools.*&&\) \\|\1 rm \-rf /tool_deps/_conda/envs/* \&\& \\|g' Dockerfile
+      - name: Build Docker image
+        run: make docker_build
+      - name: Run the newly built Docker image
+        run: |
+          make docker_run
+      - name: Check API availability
+        run: make test_api
+      - name: Run FTP tests
+        run: make test_ftp
+      - name: Install Bioblend
+        run: make install
+      - name: Run Bioblend tests
+        run: make test_bioblend

Dockerfile

@@ -1,5 +1,5 @@
 # Galaxy - Genome Annotation Suite
-FROM quay.io/bgruening/galaxy:19.09
+FROM quay.io/bgruening/galaxy:20.05
 MAINTAINER Galaxy Genome Annotation <[email protected]>
 
 WORKDIR /galaxy-central

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/galaxy-genome-annotation/docker-galaxy-genome-annotation.svg?branch=master)](https://travis-ci.org/galaxy-genome-annotation/docker-galaxy-genome-annotation)
+![Test Docker image building](https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation/workflows/Test%20Docker%20image%20building/badge.svg)
 [![Docker Repository on Quay](https://quay.io/repository/galaxy-genome-annotation/docker-galaxy-annotation/status "Docker Repository on Quay")](https://quay.io/repository/galaxy-genome-annotation/docker-galaxy-annotation)
 
 # Galaxy Image for Genome Annotation
@@ -93,7 +93,7 @@ ENV                           | Use
 ## Users & Passwords
 
 The Galaxy Admin User has the username ``[email protected]`` and the password
-``admin``. If you want to create new users, please make sure to use the ``/export/`` volume, otherwise all data will be removed whenever the container is restarted.
+``password``. If you want to create new users, please make sure to use the ``/export/`` volume, otherwise all data will be removed whenever the container is restarted.
 
 
 ## Reproducibility of Your Search Results

genome_annotation_tools_1.yml

@@ -36,7 +36,7 @@
 #  * install_repository_dependencies: True or False - whether to install repo
 #                               dependencies or not. (default: True)
 
-api_key: admin
+api_key: fakekey
 galaxy_instance: http://localhost:8080
 install_resolver_dependencies: True
 install_tool_dependencies: False

genome_annotation_tools_2.yml

@@ -36,7 +36,7 @@
 #  * install_repository_dependencies: True or False - whether to install repo
 #                               dependencies or not. (default: True)
 
-api_key: admin
+api_key: fakekey
 galaxy_instance: http://localhost:8080
 install_resolver_dependencies: True
 install_tool_dependencies: False

genome_annotation_tools_3.yml

@@ -36,18 +36,20 @@
 #  * install_repository_dependencies: True or False - whether to install repo
 #                               dependencies or not. (default: True)
 
-api_key: admin
+api_key: fakekey
 galaxy_instance: http://localhost:8080
 install_resolver_dependencies: True
 install_tool_dependencies: False
 tools:
 - name: blast_rbh
   owner: peterjc
   install_resolver_dependencies: False
+  install_repository_dependencies: False
   tool_panel_section_label: "Similarity Search"
 
 - name: blastxml_to_top_descr
   owner: peterjc
+  install_repository_dependencies: False
   tool_panel_section_label: "Similarity Search"
 
 #- name: venn_list
@@ -56,10 +58,12 @@ tools:
 
 - name: mummer
   owner: peterjc
+  install_repository_dependencies: False
   tool_panel_section_label: "Alignments"
 
 - name: mira4_assembler
   owner: peterjc
+  install_repository_dependencies: False
   tool_panel_section_label: "Assembly"
 
 - name: effectivet3