Merge pull request #3060 from martenson/remimarenco-gcc2015_talk

Add Galaxy Architecture slides in .md
2026-10-25 00:12:08 +08:00 · 2016-10-18 11:23:14 -04:00
parent 1dc2d6a4ea 564aeeccd7
commit 569723a4e5
45 changed files with 2824 additions and 4 deletions
@@ -42,6 +42,9 @@ reports_webapp.lock
 reports_webapp.log
 reports_webapp.pid

+# Jupyter Runtime Files
+.ipynb_checkpoints
+
 # Config files
 universe_wsgi.ini
 reports_wsgi.ini
@@ -14,8 +14,10 @@ PROJECT_URL?=https://github.com/galaxyproject/galaxy
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 GRUNT_EXEC?=node_modules/grunt-cli/bin/grunt
 DOCS_DIR=doc
+DOC_SOURCE_DIR=$(DOCS_DIR)/source
+SLIDESHOW_DIR=$(DOC_SOURCE_DIR)/slideshow
 OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
-
+SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'

 all: help
 	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
@@ -24,6 +26,14 @@ docs: ## generate Sphinx HTML documentation, including API docs
 	$(IN_VENV) $(MAKE) -C doc clean
 	$(IN_VENV) $(MAKE) -C doc html

+docs-slides-ready:
+	test -f plantuml.jar ||  wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
+	java -jar plantuml.jar -c $(DOC_SOURCE_DIR)/slideshow/architecture/images/plantuml_options.txt -tsvg $(SLIDESHOW_DIR)/architecture/images/ *.plantuml.txt
+	$(IN_VENV) python scripts/slideshow/build_slideshow.py 'Galaxy Architecture' $(SLIDESHOW_DIR)/architecture/galaxy_architecture.md
+
+docs-slides-export: docs-slides-ready
+	$(SLIDESHOW_TO_PDF) $(SLIDESHOW_DIR)/galaxy_architecture/galaxy_architecture.html
+
 docs-schema-ready: ## Build Github-flavored Markdown from Galaxy Tool XSD (expects libxml in environment)
 	python $(DOCS_DIR)/parse_gx_xsd.py > $(DOCS_DIR)/schema.md

@@ -33,6 +43,14 @@ docs-schema-html: docs-schema-ready ## Convert Galaxy Tool XSD Markdown docs int
 open-docs-schema: docs-schema-html ## Open HTML generated from Galaxy Tool XSD.
 	$(OPEN_RESOURCE) $(DOCS_DIR)/schema.html

+ready-slides:
+	test -f plantuml.jar ||  wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
+	java -jar plantuml.jar -c $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/plantuml_options.txt -tsvg $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/ *.plantuml.txt
+	./node_modules/mermaid/bin/mermaid.js --svg $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/server_client.mermaid --o $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images -t ./node_modules/mermaid/dist/mermaid.forest.css -c $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/sequence.json
+	./node_modules/mermaid/bin/mermaid.js --svg $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/server_client_old.mermaid --o $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images -t ./node_modules/mermaid/dist/mermaid.forest.css -c $(DOC_SOURCE_DIR)/slideshow/galaxy_architecture_2015/images/sequence.json
+
+	$(IN_VENV) python scripts/slideshow/build_slideshow.py 'Galaxy Architecture' doc/source/slideshow/galaxy_architecture_2015/galaxy_architecture_2015.md
+
 _open-docs:
 	$(OPEN_RESOURCE) $(DOCS_DIR)/_build/html/index.html

@@ -102,7 +120,7 @@ grunt-watch-develop: npm-deps ## Execute watching grunt builder for dev purposes
 	cd client && $(GRUNT_EXEC) watch --develop

 webpack-watch: npm-deps ## Execute watching webpack for dev purposes
-	cd client && ./node_modules/webpack/bin/webpack.js --watch	
+	cd client && ./node_modules/webpack/bin/webpack.js --watch

 client-develop: grunt-watch-style grunt-watch-develop webpack-watch  ## A useful target for parallel development building.
 	@echo "Remember to rerun `make client` before committing!"
@@ -15,6 +15,12 @@ import datetime
 import os
 import sys

+# Library to make .md to slideshow
+from recommonmark.parser import CommonMarkParser
+
+source_parsers = {
+    '.md': CommonMarkParser,
+}

 ####### REQUIRED GALAXY INCLUDES

@@ -43,7 +49,7 @@ templates_path = ['_templates']
 autodoc_default_flags = [ 'members', 'undoc-members', 'show-inheritance' ]

 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']

 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
@@ -0,0 +1,152 @@
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+		c0,1.242-0.438,2.298-1.312,3.162C387.003,140.369,385.954,140.802,384.73,140.802z"/>
+	<path fill="#BFBFBF" d="M394.32,132.644v7.92h-2.819v-18.688h2.819v7.935h3.399v-7.935h2.819v18.688h-2.819v-7.92H394.32z"/>
+	<path fill="#BFBFBF" d="M406.516,136.269l-0.685,4.295h-2.937l3.178-18.688h3.877l3.132,18.688h-2.964l-0.66-4.295H406.516z
+		 M407.997,126.156l-1.044,7.369h2.088L407.997,126.156z"/>
+	<path fill="#BFBFBF" d="M418.619,121.861l3.741,12.57v-12.57h2.818v18.703h-3.027l-3.877-11.978v11.978h-2.819v-18.703H418.619
+		L418.619,121.861z"/>
+	<path fill="#BFBFBF" d="M432.128,140.802c-1.243,0-2.299-0.438-3.169-1.312s-1.305-1.924-1.305-3.146v-10.2
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+		L439.033,140.564z"/>
+</g>
+<g>
+	<path fill="#BFBFBF" d="M563.609,123.877c1.569,0,2.724,0.433,3.46,1.297c0.646,0.757,0.97,1.811,0.97,3.162v2.715
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+	<path fill="#BFBFBF" d="M571.035,142.564v-18.703h8.024v2.834h-5.204v5.101h3.803v2.834h-3.803v5.102h5.204v2.834L571.035,142.564
+		L571.035,142.564z"/>
+	<path fill="#BFBFBF" d="M584.164,123.861l3.74,12.57v-12.57h2.818v18.703h-3.027l-3.877-11.978v11.978h-2.819v-18.703H584.164
+		L584.164,123.861z"/>
+	<path fill="#BFBFBF" d="M602.104,138.09c0,1.233-0.433,2.287-1.298,3.162c-0.864,0.875-1.908,1.312-3.132,1.312h-4.43v-18.703h4.43
+		c1.232,0,2.279,0.438,3.139,1.312c0.86,0.875,1.291,1.925,1.291,3.146V138.09z M596.062,139.775h1.7
+		c0.447,0,0.824-0.162,1.134-0.484c0.309-0.323,0.463-0.703,0.463-1.141v-9.785c0-0.447-0.157-0.83-0.472-1.148
+		c-0.312-0.317-0.688-0.477-1.125-0.477h-1.7V139.775z"/>
+	<path fill="#BFBFBF" d="M604.578,142.564v-18.703h8.023v2.834h-5.205v5.101h3.805v2.834h-3.805v5.102h5.205v2.834L604.578,142.564
+		L604.578,142.564z"/>
+	<path fill="#BFBFBF" d="M618.986,123.877c1.569,0,2.724,0.433,3.46,1.297c0.646,0.757,0.97,1.811,0.97,3.162v2.715
+		c0,1.322-0.503,2.44-1.507,3.355l2.088,8.158h-3.048l-1.71-7.039c-0.079,0-0.164,0-0.253,0h-1.626v7.039h-2.819v-18.688
+		L618.986,123.877L618.986,123.877z M620.672,128.381c0-1.084-0.537-1.626-1.611-1.626h-1.699v5.981h1.699
+		c0.447,0,0.828-0.16,1.142-0.479c0.312-0.316,0.471-0.7,0.471-1.147L620.672,128.381L620.672,128.381z"/>
+</g>
+</svg>
@@ -0,0 +1,23 @@
+@startuml
+
+!include plantuml_options.txt
+
+class HistoryDatasetAssociation {
+    hid: integer
+    history_id: integer
+    dataset_id: integer
+    state: string
+    name: string
+    info: string
+}
+
+class Dataset {
+    object_store_id: string
+    external_filename: string
+    _extra_files_path: string
+    file_size: integer
+    total_size: integer
+}
+
+HistoryDatasetAssociation "*" -> "1" Dataset
+@enduml
@@ -0,0 +1,29 @@
+@startuml
+
+!include plantuml_options.txt
+
+class History
+class HistoryDatasetAssociation {
+    history_content_type = 'dataset'
+    hid
+}
+class HistoryDatasetCollectionAssociation {
+    history_content_type = 'dataset_collection'
+    hid
+}
+class DatasetCollection {
+    collection_type
+}
+class DatasetCollectionElement {
+    element_index
+    element_identifier    
+}
+
+History "1" -- "*" HistoryDatasetAssociation
+History "1" -- "*" HistoryDatasetCollectionAssociation
+HistoryDatasetCollectionAssociation "1" -- "1" DatasetCollection
+DatasetCollection "1" -- "0..1" DatasetCollectionElement
+DatasetCollectionElement "*" -- "1" DatasetCollection
+HistoryDatasetAssociation "1" -- "0..1" DatasetCollectionElement
+
+@enduml
@@ -0,0 +1,28 @@
+@startuml
+
+!include plantuml_options.txt
+
+abstract class ObjectStore {
+    exists(obj)
+    file_ready(obj)
+    create(obj)
+    size(obj)
+    delete(obj)
+    get_data(obj)
+    get_filename(obj)
+    update_from_file(obj)
+    get_store_usage_percent()
+}
+
+class DiskObjectStore
+abstract class NestedObjectStore
+
+ObjectStore <|-- DiskObjectStore
+ObjectStore <|-- NestedObjectStore
+ObjectStore <|-- S3ObjectStore
+DiskObjectStore <|-- IRODSObjectStore
+NestedObjectStore <|-- DistributedObjectStore
+NestedObjectStore <|-- HierarchicalObjectStore
+
+
+@enduml
@@ -0,0 +1,34 @@
+skinparam handwritten true
+' skinparam roundcorner 20
+
+skinparam class {
+    ArrowFontColor #FFEFD5
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam object {
+    ArrowFontColor #FFEFD5
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam note {
+    BackgroundColor #FFEFD5
+    BorderColor #BF5700
+}
+
+skinparam sequence {
+    ArrowColor Orange
+    ArrowFontColor #FFEFD5
+    ActorBorderColor DarkOrange
+    ActorBackgroundColor #FFEFD5
+
+    ParticipantBorderColor DarkOrange
+    ParticipantBackgroundColor #FFEFD5
+
+    LifeLineBorderColor DarkOrange
+    LifeLineBackgroundColor #FFEFD5
+}
@@ -0,0 +1,3 @@
+{
+  "mirrorActors": false
+}
@@ -0,0 +1,20 @@
+@startuml
+
+!include plantuml_options.txt
+
+note over Browser, Server: HTTP
+
+Browser -> Server: Page Request
+activate Server
+Server -->Browser: Static Content (HTML+JS+CSS)
+deactivate Server
+
+note left of Browser: MVC with \nbackbone.js
+Browser -> Server: API Request (JSON)
+activate Server
+note right of Server: Build JSON response\nin Galaxy "API" controllers
+Server --> Browser: API Response (JSON)
+deactivate Server
+
+note left of Browser: HTML rendered from\nclient-side templates\n(in Backbone views).
+@enduml
@@ -0,0 +1,14 @@
+@startuml
+
+!include plantuml_options.txt
+
+note over Browser, Server: HTTP
+
+Browser -> Server: Page Request
+activate Server
+note right of Server: Build HTML fragments\nusing Mako Python library\nin Galaxy "web" controllers
+Server --> Browser: Static Content (HTML+JS+CSS)
+deactivate Server
+note left of Browser: Render HTML fragraments \nwith JavaScript
+
+@enduml
@@ -0,0 +1,25 @@
+@startuml
+
+!include plantuml_options.txt
+
+object webapp {
+    controllers : dict
+    api_controllers : dict
+    mapper : routes.Mapper
+    handle_request: (environ, start_response) -> ()
+    transaction_factory: (environ) -> GalaxyWebTransaction
+}
+
+object app {
+
+}
+
+object trans {
+
+}
+
+webapp -> "app" app
+app "app" <-- trans
+webapp *-- trans
+
+@enduml
@@ -0,0 +1,210 @@
+@import url(https://fonts.googleapis.com/css?family=Oxygen);
+@import url(https://fonts.googleapis.com/css?family=Consolas);
+@import url(https://fonts.googleapis.com/css?family=Droid+Serif);
+@import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
+@import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
+
+body {
+    font-family: 'Oxygen', 'PT Sans', Serif;
+}
+h1, h2, h3 {
+    font-weight: bold;
+}
+h1 {
+    font-size: 3em;
+    color: #ff9300;
+}
+h2 { font-size: 2em; }
+
+.title h1, h2 {
+    margin-bottom: 0px;
+    margin-top: 0px;
+    text-align: center;
+}
+
+.title p {
+    margin-top: 50px;
+    text-align: center;
+}
+
+.centered {
+    text-align: center;
+}
+
+img {
+    max-width: 100%;
+}
+
+.widen_image img {
+    max-width: 100%;
+    width: 100%;
+}
+
+.narrow_image img {
+    height: 500px;
+}
+
+h3 {
+    font-size: 1.8em;
+    position: absolute;
+    top: .5em;
+}
+
+.footnote {
+    position: absolute;
+    bottom: 3em;
+}
+
+.large {
+    font-size: 1.6em;
+}
+
+.larger {
+    font-size: 2em;
+}
+
+
+li p { line-height: 1.25em; }
+
+.normal {
+    font-size: 1em;
+}
+
+.smaller {
+    font-size: .8em;
+}
+
+a, a > code {
+    color: #ff9300;
+    text-decoration: none;
+}
+
+.code > pre, .code > code {
+    white-space: pre-wrap;
+}
+.remark-code, .remark-inline-code {
+    font-family: 'Consolas';
+    color: #ff9300;
+    font-size: 1.1em;
+}
+.slightly-smaller {
+    font-size: .9em;
+}
+    
+.remark-code-line-highlighted     {
+    background-color: #373832;
+}
+.pull-left {
+    float: left;
+    width: 47%;
+}
+.pull-right {
+    float: right;
+    width: 47%;
+}
+.pull-right ~ p {
+    clear: both;
+}
+#slideshow .slide .content code {
+}
+#slideshow .slide .content pre code {
+}
+
+.inverse {
+    background-color: #000;
+    background-repeat: no-repeat;
+    background-position: center;
+    background-size: contain;
+    color: #ffffff;
+}
+
+i, em, b, strong {
+    color: #ff9300;
+}
+
+.inverse h1, .inverse h2 {
+    color: #f3f3f3;
+    line-height: 0.8em;
+}
+
+.white {
+    background-color: #ffffff;
+    background-repeat: no-repeat;
+    background-position: center;
+    background-size: contain;
+    color: #000;
+}
+
+.strike {
+    text-decoration: line-through;
+}
+
+/* Slide-specific styling */
+#slide-inverse .footnote {
+    bottom: 12px;
+    left: 20px;
+}
+#slide-how .slides {
+    font-size: 0.9em;
+    position: absolute;
+    top:  151px;
+    right: 140px;
+}
+#slide-how .slides h3 {
+    margin-top: 0.2em;
+}
+#slide-how .slides .first, #slide-how .slides .second {
+    padding: 1px 20px;
+    height: 90px;
+    width: 120px;
+    -moz-box-shadow: 0 0 10px #777;
+    -webkit-box-shadow: 0 0 10px #777;
+    box-shadow: 0 0 10px #777;
+}
+#slide-how .slides .first {
+    background: #fff;
+    position: absolute;
+    top: 20%;
+    left: 20%;
+    z-index: 1;
+}
+#slide-how .slides .second {
+    position: relative;
+    background: #fff;
+    z-index: 0;
+}
+
+/* Two-column layout */
+.left-column {
+    color: #777;
+    width: 20%;
+    height: 92%;
+    float: left;
+}
+.left-column h2:last-of-type, .left-column h3:last-child {
+    color: #000;
+}
+.right-column {
+    width: 75%;
+    float: right;
+    padding-top: 1em;
+}
+
+/*First slide h1 orange, h2 white*/
+.special h1 {
+    color: #ff8800;
+}
+
+.special p {
+    color: #cbcbcb;
+}
+
+.special {
+    color: #ff8800;
+}
+
+/* Emphasis 2 */
+.special2 {
+    color: #00f900;
+}
+
@@ -99,7 +99,11 @@ def create_or_verify_database( url, galaxy_config_file, engine_options={}, app=N

 def migrate_to_current_version( engine, schema ):
    # Changes to get to current version
-    changeset = schema.changeset( None )
+    try:
+        changeset = schema.changeset( None )
+    except Exception as e:
+        log.error("Problem determining migration changeset for engine [%s]" % engine)
+        raise e
    for ver, change in changeset:
        nextver = ver + changeset.step
        log.info( 'Migrating %s -> %s... ' % ( ver, nextver ) )
@@ -0,0 +1,27 @@
+import os
+import string
+import sys
+
+
+SCRIPTS_DIRECTORY = os.path.dirname(__file__)
+TEMPLATE_PATH = os.path.join(SCRIPTS_DIRECTORY, "slideshow_template.html")
+TEMPLATE = string.Template(open(TEMPLATE_PATH, "r").read())
+
+
+def main(argv=None):
+    if argv is None:
+        argv = sys.argv
+    title = argv[1]
+    markdown_source = argv[2]
+    output = os.path.splitext(markdown_source)[0] + '.html'
+    with open(markdown_source, "r") as s:
+        content = s.read()
+    html = TEMPLATE.safe_substitute(**{
+        'title': title,
+        'content': content,
+    })
+    print html
+    open(output, "w").write(html)
+
+if __name__ == "__main__":
+    main()
@@ -0,0 +1,243 @@
+## Galaxy Tool Framework Changes
+
+This document describes changes to Galaxy's tooling framework over recent
+releases.
+
+---
+
+### 16.04
+
+Full [Galaxy changelog](https://docs.galaxyproject.org/en/master/releases/16.04_announce.html).
+
+---
+
+#### Tool Profile Version ([PR #1688](https://github.com/galaxyproject/galaxy/pull/1688))
+
+Tools may (and should) now declare a `profile` version (e.g.
+`<tool profile="16.04" ...>`).
+
+This allows Galaxy to fire a warning if a tool uses features too new for the
+current version and allows us to migrate away from some undesirable default
+behaviors that were required for backward compatiblity.
+
+---
+
+#### `set -e` by default ([d020522](https://github.com/galaxyproject/galaxy/pull/1688/commits/d020522650a9bfc86c22923a01fd5d7c07c65326))
+
+From the [IUC best practices documentation](http://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices/tool_xml.html#command-tag):
+
+> _"If you need to execute more than one shell command, concatenate them with a double ampersand (`&&`), so that an error in a command will abort the execution of the following ones."_
+
+The job script generated with profile `16.04`+ tools will include a `#set -e` statement causing this behavior by default.
+
+Older-style tools can enable this behavior by setting `strict="true"` on
+the tool `command` XML block.
+
+---
+
+#### Using Exit Codes for Error Detection ([b92074e](b92074e6ff87a19133b4d973577779c4ee6286d7))
+
+Previously the default behavior was for Galaxy to ignore exit codes and
+declare a tool in error if issued any output on standard error. This was
+a regretable default behavior and so all tools were encouraged to declare
+special XML blocks to force the use of exit codes.
+
+For any tool that declares a profile version of `16.04` or greater, the
+default is now just to use exit codes for error detection.
+
+---
+
+#### Unrobust Features Removed ([b92074e](b92074e6ff87a19133b4d973577779c4ee6286d7))
+
+A few tool features have ben removed from tools that declare a version of `16.04` or newer.
+
+- The `interepreter=` attribute on `command` blocks has been eliminated. Please use `$__tool_directory__` from within the tool instead.
+- `format="input"` on output datasets has been eliminated, please use `format_source=` to specify an exact input to derive datatype from.
+- Disables extra output file discovery by default, tools must explicitly describe the outputs to collect with `discover_dataset` tags.
+- Tools require a `version` attribute - previously an implicit default to `1.0.0` would be used.
+- `$param_file` has been eliminated.
+
+---
+
+#### Clean Working Directories
+
+Previously, Galaxy would fill tool working directories with files related to
+metadata and job metric collection. Tools will no longer be executed in the same directory as these files.
+
+This applies to all tools not just profile `16.04`+ tools.
+
+---
+
+### 16.01
+
+Full [Galaxy changelog](https://docs.galaxyproject.org/en/master/releases/16.01_announce.html).
+
+---
+
+#### Conda Dependency Resolution ([PR #1345](https://github.com/galaxyproject/galaxy/pull/1345))
+
+```xml
+<tool>
+    ...
+    <requirements>
+        <requirement type="package" version="0.11.4">FastQC</requirement>
+    </requirements>
+    ...
+</tool>
+```
+
+- Dependency resolvers tell Galaxy how to translate requirements into jobs.
+- The Conda dependency resolver forces Galaxy to create a conda environment
+  for the job with `FastQC` at version `0.11.4` installed.
+- Only dependency resolver that can be installed at runtime - great for
+  Docker images, heterogeneous clusters, and testing tools.
+- Links [Conda](http://conda.pydata.org/docs/) and [BioConda](https://bioconda.github.io/)
+
+---
+
+#### ToolBox Enhancements - Labels ([PR #1012](https://github.com/galaxyproject/galaxy/pull/1012))
+
+  ![ToolBox Labels](images/gx_toolbox_labels.png)
+
+---
+
+#### ToolBox Enhancements - Monitoring ([PR #1398](https://github.com/galaxyproject/galaxy/pull/1398))
+
+- The Galaxy toolbox can be reloaded from the Admin interface.
+- Tool conf files (e.g. `tool_conf.xml`) can be monitored and automatically
+  reloaded by Galaxy.
+- Tool conf files can now be specified as YAML (or JSON).
+
+---
+
+#### Process Inputs as JSON ([PR #1405](https://github.com/galaxyproject/galaxy/pull/1405))
+
+```xml
+    <command>python "$__tool_directory/script.py" "$json_inputs"</command>
+    <configfiles>
+        <inputs name="json_inputs" />
+    </configfiles>
+```
+
+This will produce a file referenced as `$json_inputs` that contains a nested
+JSON structure corresponding to the tools inputs. Of limitted utility for
+simple command-line tools - but complex tools with many repeats, conditional,
+and nesting could potentially benefit from this.
+
+For instance, the [JBrowse](https://github.com/galaxyproject/tools-iuc/blob/master/tools/jbrowse/jbrowse.xml)
+tool generates a complex JSON data structure using a `configfile` inside the
+XML. This is a much more portable way to deal with that.
+
+---
+
+
+#### Collections
+
+- `data_collection` tool parameters (`param`s) can now specify multiple
+  `collection_type`s for consumption ([PR #1308](https://github.com/galaxyproject/galaxy/pull/1308)).
+  - This mirrors the `format` attribute which allows a comma-separated list
+    of potential format types.
+- Multiple collections can now be supplied to a `multiple="true"` data parameter ([PR #805](https://github.com/galaxyproject/galaxy/pull/805)).
+- Output collections can specify a `type_source` attribute (again mirroring
+  `format_source`) ([PR #1153](https://github.com/galaxyproject/galaxy/pull/1153)).
+
+---
+
+### 15.10
+
+Full [Galaxy changelog](https://docs.galaxyproject.org/en/master/releases/15.10_announce.html).
+
+---
+
+#### Collections
+
+- Tools may now produce explicit nested outputs [PR #538](https://github.com/galaxyproject/galaxy/pull/538).
+  This enhances the `discover_dataset` XML tag to allow this.
+- Allow certain `output` actions on collections.
+  [PR #544](https://github.com/galaxyproject/galaxy/pull/544).
+- Allow `discover_dataset` tags to use `format` instead of `ext`
+  when referring to datatype extensions/formats.
+- Allow `min`/`max` attributes on multiple data input parameters [PR #765](https://github.com/galaxyproject/galaxy/pull/765).
+
+---
+
+#### Whitelist Tools that Generate HTML ([PR #510](https://github.com/galaxyproject/galaxy/pull/510))
+
+Galaxy now contains a plain text file that contains a list of tools whose
+output can be trusted when rendering HTML.
+
+---
+
+### 15.07
+
+Full [Galaxy changelog](https://docs.galaxyproject.org/en/master/releases/15.07_announce.html).
+
+---
+
+#### Parameterized XML Macros ([PR #362](https://github.com/galaxyproject/galaxy/pull/362))
+
+Macros now allow defining tokens to be consumed
+as XML attributes. For instance, the following definition
+
+```xml
+<tool>
+    <expand macro="inputs" foo="hello" />
+    <expand macro="inputs" foo="world" />
+    <expand macro="inputs" />
+    <macros>
+        <xml name="inputs" token_foo="the_default">
+            <inputs>@FOO@</inputs>
+        </xml>
+    </macros>
+</tool>
+```
+
+would expand out as
+
+```xml
+<tool>
+    <inputs>hello</inputs>
+    <inputs>world</inputs>
+    <inputs>the_default</inputs>
+</tool>
+```
+
+---
+
+#### Tool Form
+
+The workflow editor was updated to the use Galaxy's newer
+frontend tool form.
+
+![New Workflow Editor](images/gx_new_workflow_editor.png)
+
+---
+
+#### Environment Variables ([PR #395](https://github.com/galaxyproject/galaxy/pull/395))
+
+Tools may now use `inputs` to define environment variables that will be
+set during tool execution. The new `environment_variables` XML block is
+used to define this.
+
+```xml
+<tool>
+    ...
+    <command>
+        echo "\$INTVAR"  >  $out_file1;
+        echo "\$FORTEST" >> $out_file1;
+    </command>
+    <environment_variables>
+        <environment_variable name="INTVAR">$inttest</environment_variable>
+        <environment_variable name="FORTEST">#for i in ['m', 'o', 'o']#$i#end for#</environment_variable>
+    </environment_variables>
+    ...
+```
+
+[Test tool](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/environment_variables.xml) demonstrating the use of the `environment_variables` tag.
+
+---
+
+#### Collections
+
+ - Explicit output collections can now be used in workflows. ([PR #311](https://github.com/galaxyproject/galaxy/pull/311))
+ - The `filter` tag has been implemented for output dataset collections ([PR #455](https://github.com/galaxyproject/galaxy/pull/455). See the example tool [output_collection_filter.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/output_collection_filter.xml).
@@ -0,0 +1,18 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <title>${title}</title>
+    <meta charset="utf-8">
+    <link rel="stylesheet" type="text/css" href="style.css">
+  </head>
+  <body>
+    <textarea id="source">
+${content}
+    </textarea>
+    <script src="remark-latest.min.js">
+    </script>
+    <script>
+      var slideshow = remark.create();
+    </script>
+  </body>
+</html>
@@ -0,0 +1,25 @@
+/*
+This is a sample of a CSS file for a slideshow
+You need to put your `style.css` at the same level than your *.md slideshow file
+Example:
+MyDirectory:
+  - mySlideshow.md
+  - myCss.css
+  - images/
+*/
+@import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
+@import url(https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic);
+@import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
+
+body {
+    font-family: 'Droid Serif';
+}
+
+h1, h2, h3 {
+    font-family: 'Yanone Kaffeesatz';
+    font-weight: normal;
+}
+
+.remark-code, .remark-inline-code {
+    font-family: 'Ubuntu Mono';
+}