From 3e87c1b24618bca4b1750dade5307009963164f4 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 15 Nov 2016 14:58:04 -0500
Subject: [PATCH] Cert updates, Test updates, mutable config file updates.

---
 common/secret_vars/ssl.yml                    | 661 ++++++++++--------
 common_roles                                  |   2 +-
 .../var/integrated_tool_panel.xml             |   3 +
 .../var/shed_data_manager_conf.xml            |   2 +-
 .../var/integrated_tool_panel.xml             |  16 +
 .../var/shed_tool_data_table_conf.xml         | 160 +++++
 files/ssl/athena.galaxyproject.org_cert.pem   |  64 +-
 files/ssl/radegast.galaxyproject.org_cert.pem |  66 +-
 files/ssl/usegalaxy.org_cert.pem              |  62 +-
 files/ssl/wildcard_cert.pem                   |  32 +-
 stage/galaxy_version.yml                      |   4 +-
 .../config/job_conf.xml.j2                    |   1 +
 12 files changed, 673 insertions(+), 400 deletions(-)

diff --git a/common/secret_vars/ssl.yml b/common/secret_vars/ssl.yml
index c304b1140..a163019f7 100644
--- a/common/secret_vars/ssl.yml
+++ b/common/secret_vars/ssl.yml
@@ -1,285 +1,378 @@
 $ANSIBLE_VAULT;1.1;AES256
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diff --git a/common_roles b/common_roles
index 1182a44e2..32314d2f8 160000
--- a/common_roles
+++ b/common_roles
@@ -1 +1 @@
-Subproject commit 1182a44e2737c7a719547c29d1f86011f4dd4a59
+Subproject commit 32314d2f8844031b02156edf5236517cce410c62
diff --git a/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml b/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
index 56d7dd65f..9720bd8dc 100644
--- a/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
+++ b/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
@@ -884,6 +884,7 @@
     <section id="ncbi_blast_plus_tools" name="NCBI BLAST+" version="">
     </section>
     <section id="ngs:_assembly" name="NGS: Assembly" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.11.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.4" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/lionelguy/spades/plot_spades_stats/0.1" />
@@ -993,4 +994,6 @@
     <tool id="echo_test_bridges" />
     <tool id="echo_test_jetstream_iu" />
     <tool id="echo_test_jetstream_tacc" />
+    <section id="annotation" name="Annotation" version="">
+    </section>
 </toolbox>
diff --git a/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
index 239f04634..e3790d2fb 100644
--- a/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
+++ b/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<data_managers>
+<data_managers tool_path="/galaxy/test/shed_tools">
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download/0.0.1" id="data_manager_gemini_download" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
         <tool file="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/a580422f6f1d/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.10.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_gemini_database_downloader</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>a580422f6f1d</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.10.0</id><version>0.10.0</version></tool><data_table name="gemini_databases">  <!-- Defines a Data Table to be modified. -->
             <output> <!-- Handle the output of the Data Manager Tool -->
diff --git a/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml b/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
index ca9733882..838fd39f0 100644
--- a/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
+++ b/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
@@ -176,6 +176,22 @@
         <label id="solid" text="AB-SOLiD data" version="" />
     </section>
     <section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.6.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.3.6.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.5.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.5.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.5.0" />
diff --git a/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml b/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml
index a649d26f8..2b8e0e224 100644
--- a/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml
+++ b/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml
@@ -1720,4 +1720,164 @@
             <installed_changeset_revision>40a339e4692e</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/6aee99aec0d1/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_bam_compare</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>6aee99aec0d1</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/e22b1110529c/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_bam_coverage</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>e22b1110529c</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/4efe24a9739e/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_bam_pe_fragmentsize</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>4efe24a9739e</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/5b2abee3aff3/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_bigwig_compare</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>5b2abee3aff3</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/9ee37f06acbc/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_compute_gc_bias</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>9ee37f06acbc</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/4b3adcb7c7e9/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_compute_matrix</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>4b3adcb7c7e9</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/4eef86c1e82f/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_correct_gc_bias</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>4eef86c1e82f</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/a74111e8cbc1/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_multi_bam_summary</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>a74111e8cbc1</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/69004a60ad95/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_multi_bigwig_summary</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>69004a60ad95</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/cdde99ce71c8/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_correlation</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>cdde99ce71c8</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/71385153e5d5/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_coverage</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>71385153e5d5</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/ef2bcce0be62/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_fingerprint</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>ef2bcce0be62</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/f08d1cd387d6/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_heatmap</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>f08d1cd387d6</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/18fad2642adc/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_pca</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>18fad2642adc</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/ac1304435181/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_profile</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>ac1304435181</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="lastz_seqs">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/a1124c201eee/lastz_seqs.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>deeptools_plot_enrichment</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>a1124c201eee</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>
diff --git a/files/ssl/athena.galaxyproject.org_cert.pem b/files/ssl/athena.galaxyproject.org_cert.pem
index 8aac7972b..6d1d206da 100644
--- a/files/ssl/athena.galaxyproject.org_cert.pem
+++ b/files/ssl/athena.galaxyproject.org_cert.pem
@@ -1,36 +1,36 @@
 -----BEGIN CERTIFICATE-----
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index 28af21e1a..84e01f9f4 100644
--- a/files/ssl/radegast.galaxyproject.org_cert.pem
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index 9863169e9..429ed6781 100644
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 -----END CERTIFICATE-----
 -----BEGIN CERTIFICATE-----
 MIIF+TCCA+GgAwIBAgIQRyDQ+oVGGn4XoWQCkYRjdDANBgkqhkiG9w0BAQwFADCB
diff --git a/files/ssl/wildcard_cert.pem b/files/ssl/wildcard_cert.pem
index 993c2811a..3f1a6aa1f 100644
--- a/files/ssl/wildcard_cert.pem
+++ b/files/ssl/wildcard_cert.pem
@@ -1,21 +1,21 @@
 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----
 -----BEGIN CERTIFICATE-----
 MIIF+TCCA+GgAwIBAgIQRyDQ+oVGGn4XoWQCkYRjdDANBgkqhkiG9w0BAQwFADCB
diff --git a/stage/galaxy_version.yml b/stage/galaxy_version.yml
index ceecf0d84..c51f04b1a 100644
--- a/stage/galaxy_version.yml
+++ b/stage/galaxy_version.yml
@@ -1,4 +1,4 @@
 ---
 galaxy_version: 16.10.dev
-galaxy_commit: 2458c5455fe07c7832cb30fd5bdedc9770db6f42
-galaxy_commit_short: 2458c54
+galaxy_commit: 3ec7be27952b57cf7e0ad87fdf067cacc5e66856
+galaxy_commit_short: 3ec7be2
diff --git a/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 b/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
index e160eda95..c4d4fefd3 100644
--- a/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
+++ b/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
@@ -478,6 +478,7 @@
         <tool id="cuffquant" destination="dynamic_local_stampede_select_dynamic_walltime" handler="multi_handlers" resources="local_or_stampede"/>
         <tool id="stringtie" destination="dynamic_local_stampede_select_dynamic_walltime" handler="multi_handlers"  resources="local_or_stampede"/>
         <tool id="hisat2" destination="dynamic_local_stampede_select_dynamic_walltime" handler="multi_handlers"  resources="local_or_stampede"/>
+        <tool id="prokka" destination="dynamic_local_stampede_select_dynamic_walltime" handler="multi_handlers"  resources="local_or_stampede"/>
         <!-- bridges jobs -->
         <tool id="trinity_psc" destination="dynamic_bridges_select" handler="test_handler2" resources="bridges"/>
         <tool id="spades" destination="dynamic_bridges_select" handler="test_handler2" resources="bridges"/>