install tool - welcome

abims-sbr · Sep 15, 2020 · cf34505 · cf34505
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diff --git a/Dockerfile b/Dockerfile
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+FROM bgruening/galaxy-stable:20.05
+
+MAINTAINER ABiMS platform, [email protected]
+
+ENV GALAXY_CONFIG_BRAND EOSC-Life_D4
+
+# Install the tools
+ADD tool_list.yml $GALAXY_ROOT/tool_list.yml
+RUN install-tools $GALAXY_ROOT/tool_list.yml
+
+# Container Style
+ADD welcome.html $GALAXY_CONFIG_DIR/web/welcome.html
+
+# Mark folders as imported from the host.
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
+
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
+EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
+
+# Autostart script that is invoked during container start
+CMD ["/usr/bin/startup"]
diff --git a/README.md b/README.md
@@ -1,2 +1,27 @@
-# D4_marine_eukaryote_genomics_portal_docker
-Marine Eukaryote Genomics Portal Docker
+# Marine Eukaryote Genomics Portal Docker
+
+EOSC-Life Demonstrator 4
+
+## Docker Galaxy Stable
+This Docker container is based on the quay.io/bgruening/galaxy:20.05
+
+https://github.com/bgruening/docker-galaxy-stable
+
+## Prerequisites
+### Docker
+
+https://www.docker.com
+
+## Usage
+
+### Build the Docker image
+
+```bash
+docker build -t abims/eosc-d4 .
+docker images
+docker run  -d -p 8080:80  eosc-d4
+58e06801c2229c39aec39f06361b068bbfc84ae00cac3ede7db0bca256922822
+docker logs -f 58e06801c2229c39aec39f06361b068bbfc84ae00cac3ede7db0bca256922822
+```
+
+Access to the Galaxy instance: http://localhost:8080/
diff --git a/tool_list.yml b/tool_list.yml
@@ -0,0 +1,13 @@
+api_key: fakekey
+galaxy_instance: http://127.0.0.1:8080/
+tools:
+  - name: repeat_masker
+    owner: bgruening
+    revisions:
+      - 438f65cb1d14
+    tool_panel_section_label: Annotation
+  - name: last
+    owner: iuc
+    revisions:
+      - bf30030e5265
+    tool_panel_section_label: Last
diff --git a/welcome.html b/welcome.html
@@ -0,0 +1,57 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body style="margin: 0">
+
+    <div class="container">
+
+        <center><img src="https://www.eosc-portal.eu/sites/default/files/EOSC%20life_0.png" alt="EOSC-Life" height="400px" /></center>
+        <div style="text-align:center">
+          <h1>EOSC-Life Demonstrator 4<h1>
+          <h2>Marine Eukaryote Genomics Portal</h2>
+        </div>
+        <p>
+            For more information about:
+            <ul>
+                <li><a href="https://github.com/eosc-life/D4_marine_eukaryote_genomics_portal" target="_blank">EOSC-Life Demonstrator 4 - Marine Eukaryote Genomics Portal</a></li>
+                <li><a href="https://github.com/bgruening/docker-galaxy-stable" target="_blank">Docker Galaxy Stable</a></li>
+            </ul>
+        </p>
+        <br/>
+        <hr/>
+        <br/>
+        <div style="text-align:center">
+          <a href="https://www.embrc.eu/" target="_blank"><img src="https://www.embrc.eu/sites/embrc.eu/themes/embrc/images/logo.png" alt="EMBRC" height="100px" style="vertical-align:middle;margin:5px 5px" /></a>
+          <a href="https://www.ccmar.ualg.pt/en" target="_blank"><img src="https://www.ccmar.ualg.pt/sites/ccmar.ualg.pt/files/logos/logo_ccmar_turquesa_0.png" alt="CCMAR" height="75px" style="vertical-align:middle;margin:5px 15px"/></a>
+          <a href="http://abims.sb-roscoff.fr/" target="_blank"><img src="https://abims.sb-roscoff.fr/sites/abims.sb-roscoff.fr/files/logos/abims/abims.png" alt="ABiMS" height="75px" style="vertical-align:middle;margin:5px 15px"/></a>
+        </div>
+        <br/>
+        <hr/>
+        <br/>
+        <p class="lead">
+            <a target="_blank" class="reference" href="http://galaxyproject.org/">
+            Galaxy</a> is an open platform for supporting data intensive
+            research. Galaxy is developed by <a target="_blank" class="reference" href="http://wiki.galaxyproject.org/GalaxyTeam">The Galaxy Team</a>
+            with the support of  <a target="_blank" class="reference" href="https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTORS.md">many contributors</a>.
+            The Galaxy Docker project is supported by the University of Freiburg, part of de.NBI.
+        </p>
+
+        <footer>
+            The <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy Project</a>
+            is supported in part by <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>,
+            <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>,
+            <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>,
+            <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>,
+            <a target="_blank" class="reference" href="http://www.denbi.de">The German Network for Bioinformatics Infrastructure (de.NBI)</a>,
+            <a target="_blank" class="reference" href="http://www.jhu.edu">Johns Hopkins University</a>,
+            and <a target="_blank" class="reference" href="http://www.uni-freiburg.de">University of Freiburg</a>.
+        </footer>
+        <br/>
+        <br/>
+    </div>
+
+</body>
+</html>