From 660b92074eaf6f80bd173e462f34afb50227c055 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 23 Apr 2015 15:45:31 +0200
Subject: [PATCH 01/10] add emboss datatypes

---
 config/datatypes_conf.xml.sample | 98 ++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 42b874b46cc..3a43aebc275 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -271,6 +271,104 @@
     <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/>
     <!-- Excel datatypes -->
     <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" />
+
+    <datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="match" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Report formats http://emboss.sourceforge.net/docs/themes/ReportFormats.html -->
+    <datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="table" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Sequence formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html -->
+    <datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="phylip" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <!-- Alignment Formats http://emboss.sourceforge.net/docs/themes/AlignFormats.html -->
+    <datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="score" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="True"/>
+    <datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="True"/>
+
   </registration>
   <sniffers>
     <!--

From 72bbace9c4a2d4e68790196f351fda6ac66e05f2 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 30 Apr 2015 14:17:49 +0200
Subject: [PATCH 02/10] add debug option to the example inject command

---
 .../interactive_environments/ipython/config/ipython.ini.sample  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
index f75400fbfc2..f7a821eaab1 100644
--- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
+++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
@@ -15,7 +15,7 @@ command = docker
 image = bgruening/docker-ipython-notebook
 
 # Additional arguments that are passed to the `docker run` command.
-command_inject = --sig-proxy=true
+command_inject = --sig-proxy=true -e DEBUG=false
 
 # 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

From 618078c5c16218b6222eeb242b803c93bf15046b Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 30 Apr 2015 14:24:41 +0200
Subject: [PATCH 03/10] Refactore the configuration handling and add a new
 get_conf_dict() function.

---
 lib/galaxy/web/base/interactive_environments.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py
index 19465cf31e0..4296a829e73 100644
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -63,9 +63,9 @@ class InteractiveEnviornmentRequest(object):
         self.attr.APACHE_URLS = _boolean_option("apache_urls")
         self.attr.SSL_URLS = _boolean_option("ssl")
 
-    def write_conf_file(self, output_directory, extra={}):
+    def get_conf_dict(self, extra={}):
         """
-            Build up a configuration file that is standard for ALL IEs.
+            Build up a configuration dictionary that is standard for ALL IEs.
 
             TODO: replace hashed password with plaintext.
         """
@@ -87,7 +87,9 @@ class InteractiveEnviornmentRequest(object):
         else:
             conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/'
             web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
-            conf_file['galaxy_paster_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
+            conf_file['galaxy_web_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
+            # Galaxy paster port is deprecated
+            conf_file['galaxy_paster_port'] = conf_file['galaxy_web_port']
 
         if self.attr.PASSWORD_AUTH:
             # Generate a random password + salt
@@ -105,6 +107,13 @@ class InteractiveEnviornmentRequest(object):
             conf_file[extra_key] = extra[extra_key]
 
         self.attr.notebook_pw = notebook_pw
+        return conf_file
+
+    def write_conf_file(self, output_directory, extra={}):
+        """
+            Will create a yaml configuration file in a given output directory.
+        """
+        conf_file = self.get_conf_dict( output_directory, extra )
         # Write conf
         with open( os.path.join( output_directory, 'conf.yaml' ), 'wb' ) as handle:
             handle.write( yaml.dump(conf_file, default_flow_style=False) )

From 04b8a884bd1f94e60c6eae84f457639a15330158 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 30 Apr 2015 14:26:12 +0200
Subject: [PATCH 04/10] Pass all configuration variables to Docker using ENV,
 rather than a config file.

---
 .../ipython/templates/ipython.mako                    | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako
index 8f3a3d6655a..9c697f4dc5e 100644
--- a/config/plugins/interactive_environments/ipython/templates/ipython.mako
+++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako
@@ -11,8 +11,10 @@ ie_request.load_deploy_config()
 ie_request.attr.docker_port = 6789
 # Create tempdir in galaxy
 temp_dir = os.path.abspath( tempfile.mkdtemp() )
-# Write out conf file...needs work
-ie_request.write_conf_file(temp_dir)
+
+# Get all configurations
+conf = ie_request.get_conf_dict()
+ENV = '-e ' + ' -e '.join(['"%s=%s"' % (key.upper(), item) for key, item in conf.items()])
 
 ## IPython Specific
 # Prepare an empty notebook
@@ -34,9 +36,12 @@ else:
 notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb')
 notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree')
 
-docker_cmd = ie_request.docker_cmd(temp_dir)
+
+# Add all environment variables collected from Galaxy's IE infrastructure
+docker_cmd = ie_request.docker_cmd(temp_dir).replace('run', 'run %s' % ENV)
 ie_request.log.info("Starting IPython docker container with command [%s]" % docker_cmd)
 subprocess.call(docker_cmd, shell=True)
+
 %>
 <html>
 <head>

From 71c51e9a830f7e9f3f1e56d7a83b756ff436de01 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 30 Apr 2015 18:09:43 +0200
Subject: [PATCH 05/10] Remove write_conf_file()

---
 .../ipython/templates/ipython.mako                    |  2 +-
 lib/galaxy/web/base/interactive_environments.py       | 11 -----------
 2 files changed, 1 insertion(+), 12 deletions(-)

diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako
index 9c697f4dc5e..839e0328b33 100644
--- a/config/plugins/interactive_environments/ipython/templates/ipython.mako
+++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako
@@ -14,7 +14,7 @@ temp_dir = os.path.abspath( tempfile.mkdtemp() )
 
 # Get all configurations
 conf = ie_request.get_conf_dict()
-ENV = '-e ' + ' -e '.join(['"%s=%s"' % (key.upper(), item) for key, item in conf.items()])
+ENV = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
 
 ## IPython Specific
 # Prepare an empty notebook
diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py
index 4296a829e73..baeb32d4ba4 100644
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -7,8 +7,6 @@ import random
 from galaxy.util.bunch import Bunch
 from galaxy import web
 from galaxy import eggs
-eggs.require("PyYAML")
-import yaml
 from galaxy.managers import api_keys
 
 import logging
@@ -109,15 +107,6 @@ class InteractiveEnviornmentRequest(object):
         self.attr.notebook_pw = notebook_pw
         return conf_file
 
-    def write_conf_file(self, output_directory, extra={}):
-        """
-            Will create a yaml configuration file in a given output directory.
-        """
-        conf_file = self.get_conf_dict( output_directory, extra )
-        # Write conf
-        with open( os.path.join( output_directory, 'conf.yaml' ), 'wb' ) as handle:
-            handle.write( yaml.dump(conf_file, default_flow_style=False) )
-
     def generate_hex(self, length):
         return ''.join(random.choice('0123456789abcdef') for _ in range(length))
 

From b202c450d086590a9b5d741b8648f49e04fc06ee Mon Sep 17 00:00:00 2001
From: Eric Rasche <rasche.eric@yandex.ru>
Date: Wed, 6 May 2015 11:47:07 -0500
Subject: [PATCH 06/10] Unstage @bgruening's datatype conf changes

---
 config/datatypes_conf.xml.sample | 98 --------------------------------
 1 file changed, 98 deletions(-)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 3a43aebc275..42b874b46cc 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -271,104 +271,6 @@
     <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/>
     <!-- Excel datatypes -->
     <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" />
-
-    <datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="match" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <!-- Report formats http://emboss.sourceforge.net/docs/themes/ReportFormats.html -->
-    <datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="table" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <!-- Sequence formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html -->
-    <datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="phylip" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <!-- Alignment Formats http://emboss.sourceforge.net/docs/themes/AlignFormats.html -->
-    <datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="score" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="True"/>
-    <datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="True"/>
-
   </registration>
   <sniffers>
     <!--

From b2b25f595b3c618de4482bce6fdb791b6511c3d4 Mon Sep 17 00:00:00 2001
From: Eric Rasche <rasche.eric@yandex.ru>
Date: Wed, 6 May 2015 11:48:37 -0500
Subject: [PATCH 07/10] Update documentation on the get() function

---
 .../interactive_environments/ipython/templates/notebook.ipynb   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/interactive_environments/ipython/templates/notebook.ipynb b/config/plugins/interactive_environments/ipython/templates/notebook.ipynb
index 97c8f2970f3..f44ffb39aec 100644
--- a/config/plugins/interactive_environments/ipython/templates/notebook.ipynb
+++ b/config/plugins/interactive_environments/ipython/templates/notebook.ipynb
@@ -20,7 +20,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "You can access your data via the dataset number. For example, ``handle = get(42)``.",
+      "You can access your data via the dataset number. For example, ``handle = open(get(42), 'r')``.",
       "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.",
       "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.<br>",
       "More help and informations can be found on the project [website](https://github.com/bgruening/galaxy-ipython)."

From 8bf094ea369a40dd9bb9790150db2315e6771812 Mon Sep 17 00:00:00 2001
From: Eric Rasche <rasche.eric@yandex.ru>
Date: Wed, 6 May 2015 15:21:10 -0500
Subject: [PATCH 08/10] RStudio non-standards-compliant hacks

RStudio doesn't like lower case HTTP headers. It also doesn't like
a charset specified in content type. Thus, those get modified appropriately
and everything plays nicely
---
 lib/galaxy/web/proxy/js/lib/proxy.js | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/lib/galaxy/web/proxy/js/lib/proxy.js b/lib/galaxy/web/proxy/js/lib/proxy.js
index 242c063713e..ad4276d90e3 100644
--- a/lib/galaxy/web/proxy/js/lib/proxy.js
+++ b/lib/galaxy/web/proxy/js/lib/proxy.js
@@ -36,6 +36,23 @@ var DynamicProxy = function(options) {
 };
 
 DynamicProxy.prototype.rewriteRequest = function(request) {
+    if(request.url.indexOf('rstudio') != -1){
+        var remap = {
+            'content-type': 'Content-Type',
+            'content-length': 'Content-Length',
+        }
+        // RStudio isn't spec compliant and pitches a fit on NodeJS's http module's lowercase HTTP headers
+        for(var i = 0; i<Object.keys(remap).length; i++){
+            var key = Object.keys(remap)[i];
+            if(key in request.headers){
+                request.headers[remap[key]] = request.headers[key];
+                delete request.headers[key];
+            }
+        }
+        if('Content-Type' in request.headers && request.headers['Content-Type'] == 'application/x-www-form-urlencoded; charset=UTF-8'){
+            request.headers['Content-Type'] = 'application/x-www-form-urlencoded';
+        }
+    }
 }
 
 DynamicProxy.prototype.targetForRequest = function(request) {

From 9ab92973be879bc0a3bd40b64b0d98977a08d406 Mon Sep 17 00:00:00 2001
From: Eric Rasche <rasche.eric@yandex.ru>
Date: Thu, 7 May 2015 14:15:24 -0500
Subject: [PATCH 09/10] Remove unused import

---
 lib/galaxy/web/base/interactive_environments.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py
index 95ef4bdcc49..fddfc7aa2ef 100644
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -6,7 +6,6 @@ import random
 
 from galaxy.util.bunch import Bunch
 from galaxy import web
-from galaxy import eggs
 from galaxy.managers import api_keys
 
 import logging

From 201f2db1848964f4b3c5b5f1e172ffa03db55d32 Mon Sep 17 00:00:00 2001
From: Eric Rasche <rasche.eric@yandex.ru>
Date: Fri, 8 May 2015 17:07:04 -0500
Subject: [PATCH 10/10] Pin to :dev

---
 .../interactive_environments/ipython/config/ipython.ini.sample  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
index f7a821eaab1..b52d5760911 100644
--- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
+++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample
@@ -12,7 +12,7 @@
 command = docker
 
 # The docker image name that should be started.
-image = bgruening/docker-ipython-notebook
+image = bgruening/docker-ipython-notebook:dev
 
 # Additional arguments that are passed to the `docker run` command.
 command_inject = --sig-proxy=true -e DEBUG=false