Merge pull request #1685 from bedroesb/dockerfix3

For every topic a working Docker image

Author: bgruening

_layouts/topic.html

@@ -67,8 +67,9 @@ <h2 id="docker_image">Galaxy instances</h2>
             <p>You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.</p>
             {% if topic.docker_image and topic.docker_image != "" %}
                 <p>You can also use the following Docker image for these tutorials:</p>
-                <div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker run -d -p 8080:80 {{ topic.docker_image }}</code></pre></div></div>
-                <p>It will launch a flavored Galaxy instance available on <a href="http://localhost:8080">http://localhost:8080</a>.</p>
+                <div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker run -p 8080:80 {{ topic.docker_image }}</code></pre></div></div>
+                <p>NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.</p>
+                <p>It will launch a flavored Galaxy instance available on <a href="http://localhost:8080">http://localhost:8080</a>. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password admin to access everything.</p>
             {% endif %}
         {% endif %}
 

bin/docker-install-tutorials.sh

@@ -28,7 +28,7 @@ do
         do
             workflow-to-tools -w $w -o $dir/workflows/wftools.yaml -l $(basename $dir)
             echo " - Installing tools from workflow $(basename $w)" 
-            shed-tools install -t $dir/workflows/wftools.yaml -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD
+            shed-tools install -t $dir/workflows/wftools.yaml -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD -v
             rm $dir/workflows/wftools.yaml
         done
         echo " - Installing workflows"

topics/admin/metadata.yaml

@@ -3,7 +3,7 @@ name: "admin"
 type: "admin-dev"
 title: "Galaxy Server administration"
 summary: "Resources related to configuration and maintenance of Galaxy servers"
-docker_image: "galaxy/admin-training"
+docker_image: "quay.io/galaxy/admin-training"
 
 subtopics:
   - id: core

topics/assembly/metadata.yaml

@@ -3,7 +3,7 @@ name: "assembly"
 type: "use"
 title: "Assembly"
 summary: "DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone."
-docker_image:
+docker_image: "quay.io/galaxy/assembly-training"
 requirements:
   -
     type: "internal"

topics/computational-chemistry/metadata.yaml

@@ -3,13 +3,13 @@ name: computational-chemistry
 type: use
 title: Computational chemistry
 summary: Modelling, simulation and analysis of biomolecular systems
+docker_image: "quay.io/galaxy/computational-chemistry-training"
 
 requirements:
   -
     type: "internal"
     topic_name: introduction
 
-docker_image: "scientificomputing/bridge"
 maintainers:
   - chrisbarnettster
   - tsenapathi

topics/contributing/metadata.yaml

@@ -11,7 +11,7 @@ In 2016, the Galaxy Training Network decide to set up a new infrastructure for
 delivering easily Galaxy related training material. The idea was to develop
 something open and online based on a community effort, as always in Galaxy."
 requirements:
-docker_image:
+docker_image: "quay.io/galaxy/contributing-training"
 
 maintainers:
   - bebatut

topics/dev/metadata.yaml

@@ -3,7 +3,7 @@ name: "dev"
 type: "admin-dev"
 title: "Development in Galaxy"
 summary: "Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ..."
-docker_image:
+docker_image: "quay.io/galaxy/dev-training"
 requirements:
 maintainers:
   - lecorguille

topics/ecology/metadata.yaml

@@ -3,7 +3,7 @@ name: "ecology"
 type: "use"
 title: "Ecology"
 summary: "Learn to analyse Ecological data through Galaxy."
-docker_image:  # "quay.io/galaxy/ecology-training" # not yet ready
+docker_image: "quay.io/galaxy/ecology-training"
 edam_ontology: "topic_0610"
 
 requirements:

topics/metabolomics/metadata.yaml

@@ -3,6 +3,7 @@ name: metabolomics
 type: use
 title: Metabolomics
 summary: "Training material to analyse Mass spectrometry data in Galaxy: Metabolomics (LCMS, FIAMS, GCMS, NMR) and imaging."
+docker_image: "quay.io/galaxy/metabolomics-training"
 edam_ontology: 'topic_3172'
 requirements:
   -

topics/transcriptomics/metadata.yaml

@@ -3,7 +3,7 @@ name: transcriptomics
 type: use
 title: Transcriptomics
 summary: Training material for all kinds of transcriptomics analysis.
-docker_image: null
+docker_image: "quay.io/galaxy/transcriptomics-training"
 edam_ontology: "topic_3308"
 requirements:
   -