Merge pull request #166 from ARTbio/gks

Gks

dockerfiles/galaxy-kickstart-artimed/Dockerfile

@@ -20,5 +20,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis
            --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION \
            --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \
            --extra-vars ftp_upload_site=$IP_ADDRESS \
-           -i docker_inventory && \
+           -i inventory_files/docker && \
            /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon"

dockerfiles/galaxy-kickstart-metavisitor/Dockerfile

@@ -5,7 +5,7 @@ MAINTAINER Marius van den Beek <[email protected]>
 COPY  .  /setup
 WORKDIR /setup
 
-RUN ansible-playbook -i docker_metavisitor_inventory -c local galaxy.yml && \
+RUN ansible-playbook -i inventory_files/metavisitor -c local galaxy.yml && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9002 (supvisord web app)
@@ -20,5 +20,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis
            --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION \
            --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \
            --extra-vars ftp_upload_site=$IP_ADDRESS \
-           -i docker_metavisitor_inventory && \
+           -i inventory_files/metavisitor && \
            /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon"

dockerfiles/galaxy-kickstart-metavisitor/Dockerfile-metavisitor

@@ -12,5 +12,5 @@ EXPOSE :9002
 VOLUME ["/export", "/var/lib/docker"]
 
 CMD ansible-playbook galaxy.yml -c local --tags "persists_galaxy,nginx_config,galaxy_config_files,galaxy_extras_job_conf" --skip-tags=skip_supervisor_start_in_docker \
-           --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION -i docker_inventory && \
+           --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION -i inventory_files/docker && \
            /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon

dockerfiles/galaxy-kickstart/Dockerfile

@@ -20,12 +20,12 @@ ONBUILD  RUN  DEBIAN_FRONTEND=noninteractive  apt-get update   && \
 COPY  .  /setup
 WORKDIR /setup
 
-RUN ansible-playbook -i docker_inventory -c local galaxy.yml
+RUN ansible-playbook -i inventory_files/docker -c local galaxy.yml
 ENV LC_ALL=en_US.UTF-8 \
 LANG=en_US.UTF-8
 
 RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales
-RUN ansible-playbook -i docker_inventory -c local galaxy.yml && \
+RUN ansible-playbook -i inventory_files/docker -c local galaxy.yml && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # work around for AUFS bug
@@ -53,5 +53,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis
            --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \
            --extra-vars ftp_upload_site=$IP_ADDRESS \
            --extra-vars nat_masquerade=$NAT_MAQUERADE \
-           -i docker_inventory && \
+           -i inventory_files/docker && \
            /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon"

extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml

@@ -0,0 +1,37 @@
+tools:
+- name: data_manager_fetch_genome_dbkeys_all_fasta
+  owner: devteam
+  revisions:
+  - 776bb1b478a0
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: data_manager_bowtie_index_builder
+  owner: iuc
+  revisions:
+  - 0a0c648498e2
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: data_manager_bowtie2_index_builder
+  owner: devteam
+  revisions:
+  - e87aeff2cf88
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: data_manager_bwa_index_builder
+  owner: devteam
+  revisions:
+  - cc5ae94acf01
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: data_manager_bwa_mem_index_builder
+  owner: devteam
+  revisions:
+  - e519769cdb9c
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: data_manager_twobit_builder
+  owner: devteam
+  revisions:
+  - 74b09c8e5f6e
+  tool_panel_section_label: 'Data Managers'
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/

extra-files/galaxy-kickstart/welcome.html

@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+    <title>Homepage</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <link rel="stylesheet" href="style/base.css" type="text/css" />
+</head>
+<body>
+    <div class="document">
+        <p align="center">
+            <img src="images/galaxy-kickstart_logo.png" width="400" />
+        </p>
+    </div>
+    <div class="jumbotron">
+        <div class="container">
+            <h2>This Galaxy server instance has been set up by GalaxyKickStarter</h2>
+            <a target="_blank" href="https://artbio.github.io/ansible-artimed/" class="btn btn-primary btn-lg">GalaxyKickStarter Documentation »</a>
+            <a target="_blank" href="https://github.com/ARTbio/ansible-artimed" class="btn btn-primary btn-lg">GalaxyKickStarter Repository »</a>
+<!--            <p class="text-center"><small>Galaxy version {{ version_major.stdout }}, commit <code><a href="https://github.com/galaxyproject/galaxy/commit/{{ galaxy_changeset_id }}" target="_blank">{{ galaxy_changeset_id }}</a></code></small></p> -->
+            <br>
+            GalaxyKickStarter is developed by <a target="_blank" href="http://artbio.fr">ARTbio</a> and installed this <a target="_blank" href="https://github.com/ARTbio/galaxy/tree/galaxykickstarter">Galaxy changeset</a>
+
+			<br>
+
+            <h2>Galaxy is now running!</h2>
+
+            To customize this page edit <code>static/welcome.html</code>
+
+            <br>
+
+            <a target="_blank" href="https://wiki.galaxyproject.org/Admin/Config" class="btn btn-primary btn-lg">Configuring Galaxy »</a>
+            <a target="_blank" href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial" class="btn btn-primary btn-lg">Installing Tools »</a>
+
+        </div>
+    </div>
+
+
+
+    <div class="container">
+        <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>.
+        </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>,
+            and <a target="_blank" class="reference" href="http://www.jhu.edu/">Johns Hopkins University</a>.
+        </footer>
+
+    </div>
+
+
+</body>
+</html>

group_vars/kickstart

@@ -0,0 +1,5 @@
+galaxy_tools_tool_list_files:
+  - "extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml"
+additional_files_list:
+  - { src: "extra-files/galaxy-kickstart/welcome.html", dest: "{{ galaxy_server_dir }}/static/" }
+  - { src: "extra-files/galaxy-kickstart/galaxy-kickstart_logo.png", dest: "{{ galaxy_server_dir }}/static/images/" }

inventory_files/artimed

@@ -0,0 +1,5 @@
+[artimed]
+localhost ansible_connection=local
+
+# change to the line below if remote target host
+# <remote host IP> ansible_ssh_user="root" ansible_ssh_private_key_file="<path/to/your/private/key>"

inventory_files/aws

@@ -0,0 +1,7 @@
+[aws]
+# adapt the lines below by putting your aws IP and private key to make FTP work in the default AWS VPC (Virtual Private Cloud).
+<target Amazon Web Services IP address> ansible_ssh_user="<user (may be 'ubuntu')>" ansible_ssh_private_key_file="<path/to/your/aws/private/key.pem>"
+
+# *In addition*, adapt the group-specific variables below (here [kickstart], but you can change it, e.g [metavisitor])
+[kickstart]
+<target Amazon Web Services IP address> ansible_ssh_user="<user (may be 'ubuntu')>" ansible_ssh_private_key_file="<path/to/your/aws/private/key.pem>"

inventory_files/docker

@@ -0,0 +1,2 @@
+[docker]
+localhost ansible_connection=local

inventory_files/galaxy-kickstart

@@ -0,0 +1,5 @@
+[kickstart]
+localhost ansible_connection=local
+
+# if remote target, replace the above line by
+# <remote host IP> ansible_ssh_user="root" ansible_ssh_private_key_file="<path/to/your/private/key>"

inventory_files/metavisitor

@@ -0,0 +1,5 @@
+[metavisitor]
+localhost ansible_connection=local
+
+# change with the line bellow if remote target host
+# <remote host IP> ansible_ssh_user="root" ansible_ssh_private_key_file="<path/to/your/private/key>"

inventory_files/vagrant

@@ -0,0 +1,5 @@
+# use this inventory file to target a VM set up using vagrant
+# adapt the group variable (here [kickstart]) as you wish
+
+[kickstart]
+localhost ansible_ssh_user="vagrant" ansible_port=2222 ansible_private_key_file="~/ansible-artimed/.vagrant/machines/default/virtualbox/private_key"