1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/172e1713535c/
Changeset: 172e1713535c
User: greg
Date: 2014-05-20 23:13:26
Summary: Only load the tool panel if in Galaxy.
Affected #: 1 file
diff -r c5e14473dfb79328f077d81a6cafd9c8a07ffe23 -r 172e1713535c24cc6c07caa5f90494b68827b638 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -145,7 +145,7 @@
self.init_tools( config_filename )
except:
log.exception( "Error loading tools defined in config %s", config_filename )
- if self.integrated_tool_panel_config_has_contents:
+ if self.app.name == 'galaxy' and self.integrated_tool_panel_config_has_contents:
# Load self.tool_panel based on the order in self.integrated_tool_panel.
self.load_tool_panel()
if app.config.update_integrated_tool_panel:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c5e14473dfb7/
Changeset: c5e14473dfb7
User: jmchilton
Date: 2014-05-20 23:07:43
Summary: Document install_database_connection in universe_wsgi.ini.
Affected #: 1 file
diff -r 622d4d3ed3bdb34edeca089a0775cdff86114798 -r c5e14473dfb79328f077d81a6cafd9c8a07ffe23 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -118,6 +118,14 @@
# 'galaxy.model.orm.logging_connection_proxy'
#database_query_profiling_proxy = False
+# By default, Galaxy will use the same database to track user data and
+# tool shed install data. There are many situtations in which it is
+# valuable to seperate these - for instance bootstrapping fresh Galaxy
+# instances with pretested installs. The following optin can be used to
+# separate the tool shed install database (all other options listed above
+# but prefixed with install_ are also available).
+#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
+
# -- Files and directories
# Path where genome builds are stored. This defaults to tool-data/genome
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ff42e7cdcd97/
Changeset: ff42e7cdcd97
Branch: next-stable
User: jmchilton
Date: 2014-05-20 22:31:14
Summary: Enable job metrics by default.
They should work with all stock Galaxy runners now.
Affected #: 1 file
diff -r b814c23924470203ff3f37b28066a118e75bf348 -r ff42e7cdcd9716324c7b423135f24b44d327168c run.sh
--- a/run.sh
+++ b/run.sh
@@ -19,6 +19,7 @@
data_manager_conf.xml.sample
shed_data_manager_conf.xml.sample
openid_conf.xml.sample
+ job_metrics_conf.xml.sample
universe_wsgi.ini.sample
tool-data/shared/ncbi/builds.txt.sample
tool-data/shared/ensembl/builds.txt.sample
https://bitbucket.org/galaxy/galaxy-central/commits/e49feb93943d/
Changeset: e49feb93943d
Branch: next-stable
User: jmchilton
Date: 2014-05-20 22:31:14
Summary: Fix up job_conf.xml env element logging.
Now works with all runners.
Affected #: 1 file
diff -r ff42e7cdcd9716324c7b423135f24b44d327168c -r e49feb93943da7c6a1ccb84d6dff4518742282a8 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -104,12 +104,11 @@
</destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="java_cluster" runner="drmaa">
- <!-- set arbitrary environment variables at runtime - like metrics
- doesn't yet work with local or CLI runners. But should work with
- DRMAA/SLURM, PBS, Condor, and LWR. General dependencies for tools
- should be configured via tool_dependency_dir and package options
- and these options should be reserved for defining cluster specific
- options.
+ <!-- set arbitrary environment variables at runtime. General
+ dependencies for tools should be configured via
+ tool_dependency_dir and package options and these
+ options should be reserved for defining cluster
+ specific options.
--><env id="_JAVA_OPTIONS">-Xmx=6GB</env><env id="ANOTHER_OPTION" raw="true">'5'</env><!-- raw disables auto quoting -->
https://bitbucket.org/galaxy/galaxy-central/commits/622d4d3ed3bd/
Changeset: 622d4d3ed3bd
User: jmchilton
Date: 2014-05-20 22:31:43
Summary: Merge next-stable.
Affected #: 2 files
diff -r 70400d62e299e041b18e934788fc34ad7bfc2ddb -r 622d4d3ed3bdb34edeca089a0775cdff86114798 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -104,12 +104,11 @@
</destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="java_cluster" runner="drmaa">
- <!-- set arbitrary environment variables at runtime - like metrics
- doesn't yet work with local or CLI runners. But should work with
- DRMAA/SLURM, PBS, Condor, and LWR. General dependencies for tools
- should be configured via tool_dependency_dir and package options
- and these options should be reserved for defining cluster specific
- options.
+ <!-- set arbitrary environment variables at runtime. General
+ dependencies for tools should be configured via
+ tool_dependency_dir and package options and these
+ options should be reserved for defining cluster
+ specific options.
--><env id="_JAVA_OPTIONS">-Xmx=6GB</env><env id="ANOTHER_OPTION" raw="true">'5'</env><!-- raw disables auto quoting -->
diff -r 70400d62e299e041b18e934788fc34ad7bfc2ddb -r 622d4d3ed3bdb34edeca089a0775cdff86114798 run.sh
--- a/run.sh
+++ b/run.sh
@@ -19,6 +19,7 @@
data_manager_conf.xml.sample
shed_data_manager_conf.xml.sample
openid_conf.xml.sample
+ job_metrics_conf.xml.sample
universe_wsgi.ini.sample
tool-data/shared/ncbi/builds.txt.sample
tool-data/shared/ensembl/builds.txt.sample
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b814c2392447/
Changeset: b814c2392447
Branch: next-stable
User: dannon
Date: 2014-05-20 18:06:07
Summary: Clarify default option (no quotes) for amqp_internal_connection
Affected #: 1 file
diff -r 8b66d43bc2d1e2119baa7589b6721e360840948e -r b814c23924470203ff3f37b28066a118e75bf348 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -831,7 +831,7 @@
# will automatically create and use a separate sqlite database located in your
# <galaxy>/database folder (indicated in the commented out line below).
-#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE"
+#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
https://bitbucket.org/galaxy/galaxy-central/commits/70400d62e299/
Changeset: 70400d62e299
User: dannon
Date: 2014-05-20 18:06:21
Summary: Merge next-stable.
Affected #: 1 file
diff -r 512424a01563a2427fc0ff6225fde2737edc6900 -r 70400d62e299e041b18e934788fc34ad7bfc2ddb universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -831,7 +831,7 @@
# will automatically create and use a separate sqlite database located in your
# <galaxy>/database folder (indicated in the commented out line below).
-#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE"
+#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8b66d43bc2d1/
Changeset: 8b66d43bc2d1
Branch: next-stable
User: dannon
Date: 2014-05-20 17:55:24
Summary: When using AMQP, if the AMQP server goes down this will now more nicely catch the Connection refused error in send_control_task
Affected #: 1 file
diff -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef -r 8b66d43bc2d1e2119baa7589b6721e360840948e lib/galaxy/queue_worker.py
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -70,11 +70,16 @@
'kwargs': kwargs}
if noop_self:
payload['noop'] = trans.app.config.server_name
- c = Connection(trans.app.config.amqp_internal_connection)
- with producers[c].acquire(block=True) as producer:
- producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
- declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
- routing_key='control')
+ try:
+ c = Connection(trans.app.config.amqp_internal_connection)
+ with producers[c].acquire(block=True) as producer:
+ producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
+ declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
+ routing_key='control')
+ except Exception:
+ # This is likely connection refused.
+ # TODO Use the specific Exception above.
+ log.exception("Error sending control task: %s." % payload)
# Tasks -- to be reorganized into a separate module as appropriate. This is
https://bitbucket.org/galaxy/galaxy-central/commits/512424a01563/
Changeset: 512424a01563
User: dannon
Date: 2014-05-20 17:55:54
Summary: Merge next-stable.
Affected #: 1 file
diff -r 37509e01ee5db4b0552537c77f3771b9671e5dae -r 512424a01563a2427fc0ff6225fde2737edc6900 lib/galaxy/queue_worker.py
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -70,11 +70,16 @@
'kwargs': kwargs}
if noop_self:
payload['noop'] = trans.app.config.server_name
- c = Connection(trans.app.config.amqp_internal_connection)
- with producers[c].acquire(block=True) as producer:
- producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
- declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
- routing_key='control')
+ try:
+ c = Connection(trans.app.config.amqp_internal_connection)
+ with producers[c].acquire(block=True) as producer:
+ producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
+ declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
+ routing_key='control')
+ except Exception:
+ # This is likely connection refused.
+ # TODO Use the specific Exception above.
+ log.exception("Error sending control task: %s." % payload)
# Tasks -- to be reorganized into a separate module as appropriate. This is
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.