Upgrade the Galaxy version on GVL 4.1 to Galaxy 17.01

This will switch to the Galaxy Project's release branch of the git repo from the GVL project's Galaxy fork.

Note: This will remove the genomespace setup for this machine.
There is a git diff listed at the bottom of this procedure to help with restoration of genomespace functionality but it has yet to be tested.

Add Galaxy project galaxy repo as upstream.

sudo su galaxy
cd /mnt/galaxy/galaxy-app

Set the username and email for the git operations..

git config --global user.email "<git_user_email>"
git config --global user.name "<git_username>"

Then I did a status to see where I was at.

git status

There were some changed files but they were inconsequential.. So I stashed the changes.

git stash
git status

Now just shows some untracked changes (mainly static pages and logos etc)

branch: GVL 4.1.0.alpha

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	database/template_cache/
	lib/galaxy/jobs/rules/dyndests.py
	reports.conf.d/
	scripts/api/manage_bootstrap_user.py
	scripts/install_tool_shed_tools.py
	scripts/manage_bootstrap_user.py
	static/images/EMBL_Australia_logo.png
	static/images/Nectar_logo.jpeg
	static/images/RDSILOGO.jpg
	static/images/UOM-Rev3D_S_SmRBG.jpg
	static/images/ands-logo.jpg
	static/images/cloud.gif
	static/images/cloud_text.png
	static/images/embl.png
	static/images/gvl.png
	static/images/logo_uom.png
	static/images/nectardirectorate-footer-logo.png
	static/images/vlsci-logo.gif
	tool-data/fastx_clipper_sequences.txt
	tool-data/gatk2_annotations.txt
	tool-data/shared/ncbi/
	tool_list.yaml

Now list the remotes.

git remote -v

origin	https://github.com/gvlproject/galaxy (fetch)
origin	https://github.com/gvlproject/galaxy (push)

Add the Galaxy project upstream

git remote add upstream https://github.com/galaxyproject/galaxy
git remote -v

origin	https://github.com/gvlproject/galaxy (fetch)
origin	https://github.com/gvlproject/galaxy (push)
upstream	https://github.com/galaxyproject/galaxy (fetch)
upstream	https://github.com/galaxyproject/galaxy (push)

List all the branches

git branch -a

* gvl_4.1.0_alpha
  remotes/origin/HEAD -> origin/dev
  remotes/origin/dev
  remotes/origin/genomespace_workflows
  remotes/origin/gvl
  remotes/origin/gvl_4.0.0
  remotes/origin/gvl_4.0.0_genomespace
  remotes/origin/gvl_4.1.0_alpha
  remotes/origin/martenson-patch-1
  remotes/origin/master
  remotes/origin/release_13.01
  remotes/origin/release_13.02
  remotes/origin/release_13.04
  remotes/origin/release_13.06
  remotes/origin/release_13.08
  remotes/origin/release_13.11
  remotes/origin/release_14.02
  remotes/origin/release_14.04
  remotes/origin/release_14.06
  remotes/origin/release_14.08
  remotes/origin/release_14.10
  remotes/origin/release_15.01
  remotes/origin/release_15.03
  remotes/origin/release_15.05

Pull in the upstream branches

git pull upstream

List the branches again

git branch -a

* gvl_4.1.0_alpha
  remotes/origin/HEAD -> origin/dev
  remotes/origin/dev
  remotes/origin/genomespace_workflows
  remotes/origin/gvl
  remotes/origin/gvl_4.0.0
  remotes/origin/gvl_4.0.0_genomespace
  remotes/origin/gvl_4.1.0_alpha
  remotes/origin/martenson-patch-1
  remotes/origin/master
  remotes/origin/release_13.01
  remotes/origin/release_13.02
  remotes/origin/release_13.04
  remotes/origin/release_13.06
  remotes/origin/release_13.08
  remotes/origin/release_13.11
  remotes/origin/release_14.02
  remotes/origin/release_14.04
  remotes/origin/release_14.06
  remotes/origin/release_14.08
  remotes/origin/release_14.10
  remotes/origin/release_15.01
  remotes/origin/release_15.03
  remotes/origin/release_15.05
  remotes/upstream/dev
  remotes/upstream/master
  remotes/upstream/master-toolshed
  remotes/upstream/release_13.01
  remotes/upstream/release_13.02
  remotes/upstream/release_13.04
  remotes/upstream/release_13.06
  remotes/upstream/release_13.08
  remotes/upstream/release_13.11
  remotes/upstream/release_14.02
  remotes/upstream/release_14.04
  remotes/upstream/release_14.06
  remotes/upstream/release_14.08
  remotes/upstream/release_14.10
  remotes/upstream/release_15.01
  remotes/upstream/release_15.03
  remotes/upstream/release_15.05
  remotes/upstream/release_15.07
  remotes/upstream/release_15.10
  remotes/upstream/release_16.01
  remotes/upstream/release_16.04
  remotes/upstream/release_16.07
  remotes/upstream/release_16.10
  remotes/upstream/release_17.01
  remotes/upstream/revert-3572-fix_3548

Now switch to the galaxyproject 17.01 release

git checkout upstream/release_17.01

git status

HEAD detached at upstream/release_17.01
Untracked files:
  (use "git add <file>..." to include in what will be committed)

	database/template_cache/
	lib/galaxy/jobs/rules/dyndests.py
	reports.conf.d/
	scripts/api/manage_bootstrap_user.py
	scripts/install_tool_shed_tools.py
	scripts/manage_bootstrap_user.py
	static/images/EMBL_Australia_logo.png
	static/images/Nectar_logo.jpeg
	static/images/RDSILOGO.jpg
	static/images/UOM-Rev3D_S_SmRBG.jpg
	static/images/ands-logo.jpg
	static/images/cloud.gif
	static/images/cloud_text.png
	static/images/embl.png
	static/images/gvl.png
	static/images/logo_uom.png
	static/images/nectardirectorate-footer-logo.png
	static/images/vlsci-logo.gif
	tool-data/fastx_clipper_sequences.txt
	tool-data/gatk2_annotations.txt
	tool-data/shared/ncbi/
	tool_list.yaml

git log

Should show all the commit history for the 17.01 branch

Now we need to stop galaxy..

from the galaxy directory (/mnt/galaxy/galaxy-app/)

./run.sh --pid-file=main.pid --log-file=main.log --stop-daemon

upgrade the database

sh manage_db.sh upgrade

Add the following line to the bottom of the galaxy.ini file in /mnt/galaxy/galaxy-app/config/galaxy.ini

conda_auto_init = True

start galaxy again

./run.sh --pid-file=main.pid --log-file=main.log --daemon

Everything should work! (Except Genomespace but this can be fixed by reapplying the diff below...) NOTE: This bit has yet to be tested...

diff --git a/client/galaxy/scripts/mvc/tool/tool-genomespace.js b/client/galaxy/scripts/mvc/tool/tool-genomespace.js
index 1606f178b..d4adff81e 100644
--- a/client/galaxy/scripts/mvc/tool/tool-genomespace.js
+++ b/client/galaxy/scripts/mvc/tool/tool-genomespace.js
@@ -4,7 +4,7 @@ define([], function() {
 // tool form templates
 return {
     openFileBrowser: function( options ) {
-        var GS_UPLOAD_URL = "https://gsui.genomespace.org/jsui/upload/loadUrlToGenomespace.html?getLocation=true";
+        var GS_UPLOAD_URL = "https://genomespace.genome.edu.au/jsui/upload/loadUrlToGenomespace.html?getLocation=true";

         var newWin = window.open(GS_UPLOAD_URL, "GenomeSpace File Browser", "height=360px,width=600px");

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index a9d714cdf..159cda17f 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -395,7 +395,7 @@
     <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" edam_format="format_1936"/>
+    <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True" edam_format="format_1936" display_in_upload="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"/>
diff --git a/lib/galaxy/web/form_builder.py b/lib/galaxy/web/form_builder.py
index aa86c9cd9..13207fdbb 100644
--- a/lib/galaxy/web/form_builder.py
+++ b/lib/galaxy/web/form_builder.py
@@ -246,7 +246,7 @@ class GenomespaceFileField(BaseField):
         self.value = value or ""

     def get_html(self, prefix=""):
-        return unicodify('<script src="https://gsui.genomespace.org/jsui/upload/gsuploadwindow.js"></script>'
+        return unicodify('<script src="https://genomespace.genome.edu.au/jsui/upload/gsuploadwindow.js"></script>'
                          '<input type="text" name="{0}{1}" value="{2}">&nbsp;'
                          '<a href="javascript:gsLocationByGet({{ successCallback: function(config)'
                          ' {{ selector_name = \'{0}{1}\'; selector = \'input[name=\' + selector_name.replace(\'|\', \'\\\\|\') + \']\';'
diff --git a/openid/genomespace.xml b/openid/genomespace.xml
index 65bf95ecb..983f31807 100644
--- a/openid/genomespace.xml
+++ b/openid/genomespace.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <provider id="genomespace" name="GenomeSpace">
-    <op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url>
+    <op_endpoint_url>https://genomespace.genome.edu.au/identityServer/xrd.jsp</op_endpoint_url>
     <sreg>
         <field name="nickname" required="True">
             <use_for name="username"/>

diff --git a/tools/data_source/ucsc_tablebrowser.xml b/tools/data_source/ucsc_tablebrowser.xml
index f93aca608..8dac1c17d 100644
--- a/tools/data_source/ucsc_tablebrowser.xml
+++ b/tools/data_source/ucsc_tablebrowser.xml
@@ -4,10 +4,10 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" version="1.0.0">
+<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source">
     <description>table browser</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="https://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
+    <inputs action="http://ucsc.genome.edu.au/cgi-bin/hgTables" check_values="false" method="get">
         <display>go to UCSC Table Browser $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
         <param name="tool_id" type="hidden" value="ucsc_table_direct1" />
@@ -39,8 +39,4 @@
         <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
     </outputs>
     <options sanitize="False" refresh="True"/>
-    <citations>
-        <citation type="doi">10.1093/database/bar011</citation>
-        <citation type="doi">10.1101/gr.229102</citation>
-    </citations>
-</tool>
+</tool>

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galaxy_17.01_upgrade.md

galaxy_17.01_upgrade.md

Upgrade the Galaxy version on GVL 4.1 to Galaxy 17.01

Add Galaxy project galaxy repo as upstream.

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galaxy_17.01_upgrade.md

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Upgrade the Galaxy version on GVL 4.1 to Galaxy 17.01

Add Galaxy project galaxy repo as upstream.