Merge pull request #3330 from bgruening/hicbrowser

HiCBrowser as Galaxy IE
2026-09-24 16:30:27 +08:00 · 2017-09-08 14:18:18 +02:00
parent f623613a39 d80ecbd7a7
commit 508fdb9d2b
5 changed files with 133 additions and 0 deletions
@@ -0,0 +1,11 @@
+# This file lists acceptable images to allow runing.
+#
+# This allows you, the admin, to create multiple flavours
+# for your users to run. E.g. maybe you need a specific branded flavour,
+# you can create the image based on our default image and add the
+# appropriate files.
+---
+-
+    image: bgruening/docker-hicbrowser
+    description: |
+        A simple web browser to visualize Hi-C and other genomic tracks
@@ -0,0 +1,46 @@
+[main]
+# Following options are ignored if using the Galaxy dynamic proxy but
+# are useful if mapping a range of ports for environment consumption.
+#password_auth = False
+#ssl = False
+
+[docker]
+# Command to launch docker container. For example `sudo docker` or `docker-lxc`.
+# If you need to use a command like `sg` you can do that here, just be sure to
+# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
+#
+# It is recommended that you use command_inject if you need to inject
+# additional parameters. This command string is re-used for a `docker inspect`
+# command and will likely cause errors if it is extensively modified, past the
+# usual group/sudo changes.
+#command = docker {docker_args}
+
+# The image argument was moved to "allowed_images.yml.sample"
+
+# Additional arguments that are passed to the `docker run` command.
+command_inject = --sig-proxy=true -e DEBUG=false -e KILL_MODE=True -e DEFAULT_CONTAINER_RUNTIME=120
+
+# URL to access the Galaxy API with from the spawn Docker containter, if empty
+# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
+# Docker host of the spawned container if that is also not set.
+#galaxy_url =
+
+# The Docker hostname. It can be useful to run the Docker daemon on a different
+# host than Galaxy.
+#docker_hostname = localhost
+
+# Try to set the tempdirectory to world execute - this can fix the issue 
+# where 'sudo docker' is not able to mount the folder otherwise.
+# "finalize namespace chdir to /import permission denied"
+#wx_tempdir = False
+
+# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
+# located on an NFS share, which does not work well as Docker volume. In this case
+# you can have a shared sshfs share which you can use as temporary directory to
+# share data between the IE and Galaxy.
+#docker_galaxy_temp_dir = None
+
+# If your Docker container exposes more then one port, Galaxy needs to know to
+# which ports it needs to connect. With this option you can specify the port number
+# inside your container to which Galaxy should connect.
+docker_connect_port = 80
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
+<interactive_environment name="HiCBrowser">
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">binary.CompressedArchive</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">hicbrowser.mako</entry_point>
+</interactive_environment>
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+// Load an interactive environment (IE) from a remote URL
+// @param {String} hicexplorer_access_url: the URL embeded in the page and loaded
+function load_hicexplorer(hicexplorer_access_url){
+    // When the page has completely loaded...
+    $( document ).ready(function() {
+        // Test if we can access the GIE, and if so, execute the function
+        // to load the GIE for the user.
+        test_ie_availability(hicexplorer_access_url, function(){
+            append_notebook(hicexplorer_access_url);
+        });
+    });
+}
@@ -0,0 +1,49 @@
+<%namespace name="ie" file="ie.mako" />
+<%
+    # Sets ID and sets up a lot of other variables
+    ie_request.load_deploy_config()
+
+    # Define a volume that will be mounted into the container.
+    # This is a useful way to provide access to large files in the container,
+    # if the user knows ahead of time that they will need it.
+
+    import os
+    mount_path = hda.file_name
+    data_vol = ie_request.volume(mount_path, '/data/data_pack.tar.gz', how='rw')
+
+    # Add all environment variables collected from Galaxy's IE infrastructure
+    # Launch the IE.
+
+    ie_request.launch(
+       image = trans.request.params.get('image_tag', None),
+       additional_ids = trans.request.params.get('additional_dataset_ids', None),
+       volumes = [data_vol]
+    )
+
+    # Only once the container is launched can we template our URLs. The ie_request
+    # doesn't have all of the information needed until the container is running.
+
+    url = ie_request.url_template('${PROXY_URL}')
+
+%>
+<html>
+<head>
+    ${ ie.load_default_js() }
+</head>
+<body>
+<script type="text/javascript">
+
+    ${ ie.default_javascript_variables() }
+    var url = '${ url }';
+    ${ ie.plugin_require_config() }
+
+
+    requirejs(['interactive_environments', 'plugin/hicbrowser'], function () {
+        load_hicexplorer(url);
+    });
+
+</script>
+<div id="main" width="100%" height="100%">
+</div>
+</body>
+</html>