1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4bcf8ca400ae/
Changeset: 4bcf8ca400ae
User: jgoecks
Date: 2014-07-02 00:36:28
Summary: Trackster: disable mousewheel scrolling for now until a better usage model can be created.
Affected #: 1 file
diff -r 7ecbf85f918180a1ed415629968c763441bb0869 -r 4bcf8ca400aee4f72900de8a375707256f0ae369 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1070,6 +1070,11 @@
d.current_x = d.offsetX;
var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low));
view.move_delta(delta_chrom);
+ })
+ /*
+ FIXME: Do not do this for now because it's too jittery. Some kind of gravity approach is
+ needed here because moving left/right should be difficult.
+
// Also capture mouse wheel for left/right scrolling
}).bind( 'mousewheel', function( e, d, dx, dy ) {
// Only handle x axis scrolling; y axis scrolling is
@@ -1079,6 +1084,7 @@
view.move_delta( delta_chrom );
}
});
+ */
// Dragging in the top label track allows selecting a region to zoom in on selected region.
this.top_labeltrack.bind( "dragstart", function( e, d ) {
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/7ecbf85f9181/
Changeset: 7ecbf85f9181
User: jgoecks
Date: 2014-07-02 00:27:15
Summary: Fixes for Trackster and Circster, mostly around preference selection and usage.
Affected #: 4 files
diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/utils/config.js
--- a/static/scripts/utils/config.js
+++ b/static/scripts/utils/config.js
@@ -32,7 +32,7 @@
* Cast and set value. This should be instead of
* setting.set('value', new_value)
*/
- set_value: function(value) {
+ set_value: function(value, options) {
var type = this.get('type');
if (type === 'float') {
@@ -43,7 +43,7 @@
}
// TODO: handle casting from string to bool?
- this.set('value', value);
+ this.set({value: value}, options);
}
}, {
// This is a master list of default settings for known settings.
@@ -101,10 +101,10 @@
/**
* Set value for a setting.
*/
- set_value: function(key, value) {
+ set_value: function(key, value, options) {
var s = this.get(key);
if (s) {
- return s.set_value(value);
+ return s.set_value(value, options);
}
return undefined;
diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/circster.js
--- a/static/scripts/viz/circster.js
+++ b/static/scripts/viz/circster.js
@@ -620,8 +620,13 @@
$.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {
// Set bounds.
self.data_bounds = self.get_data_bounds(genome_wide_data);
- track.get('config').set_value('min_value', self.data_bounds[0]);
- track.get('config').set_value('max_value', self.data_bounds[1]);
+
+ // Set min, max value in config so that they can be adjusted. Make this silent
+ // because these attributes are watched for changes and the viz is updated
+ // accordingly (set up in initialize). Because we are setting up, we don't want
+ // the watch to trigger events here.
+ track.get('config').set_value('min_value', self.data_bounds[0], {silent: true});
+ track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});
// Merge chroms layout with data.
layout_and_data = _.zip(chrom_arcs, genome_wide_data),
diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -994,7 +994,8 @@
};
}));
});
- }
+ },
+ minLength: 2
});
});
if (this.vis_id !== undefined) {
diff -r b38a6f5e042bcad4beb40c3df51d4fe162258575 -r 7ecbf85f918180a1ed415629968c763441bb0869 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -894,7 +894,7 @@
// -- Set up config settings. --
var models = [
- { key: 'name', value: this.get('dataset').get('name') },
+ { key: 'name', default_value: this.get('dataset').get('name') },
{ key: 'color' },
{ key: 'min_value', label: 'Min Value', type: 'float', default_value: 0 },
{ key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 }
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/1d6e0f352bfe/
Changeset: 1d6e0f352bfe
User: jmchilton
Date: 2014-07-01 14:07:09
Summary: Bugfix: Value error when specifying empty docker_volume param.
Thanks Andrew Stewart!
Affected #: 1 file
diff -r 2e1de0fc5a3cacf0e7caf64963145fc59b239c7e -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e lib/galaxy/tools/deps/containers.py
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -204,6 +204,9 @@
)
def __expand_str(self, value):
+ if not value:
+ return value
+
template = string.Template(value)
variables = dict()
https://bitbucket.org/galaxy/galaxy-central/commits/b38a6f5e042b/
Changeset: b38a6f5e042b
User: jmchilton
Date: 2014-07-01 14:07:09
Summary: Allow Docker destinations to use --volumes-from option.
Enables certain kind of Docker-to-Docker job executions. Thanks to Andrew Stewart.
Affected #: 3 files
diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -154,6 +154,11 @@
are available to all jobs and $job_directory is also available for
Pulsar jobs.
-->
+ <!-- One can run docker using volumes-from tag by setting the following
+ parameter. For more information on volumes-from check out the following
+ docker tutorial. https://docs.docker.com/userguide/dockervolumes/
+ -->
+ <!-- <param id="docker_volumes_from">parent_container_name</param> --><!-- Control memory allocatable by docker container with following option:
--><!-- <param id="docker_memory">24G</param> -->
diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 lib/galaxy/tools/deps/containers.py
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -190,10 +190,12 @@
volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults"))
# TODO: Remove redundant volumes...
volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
+ volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
return docker_util.build_docker_run_command(
command,
self.container_id,
volumes=volumes,
+ volumes_from=volumes_from,
env_directives=env_directives,
working_directory=working_directory,
docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND),
diff -r 1d6e0f352bfe1db4b1e23ade889d72473054c73e -r b38a6f5e042bcad4beb40c3df51d4fe162258575 lib/galaxy/tools/deps/docker_util.py
--- a/lib/galaxy/tools/deps/docker_util.py
+++ b/lib/galaxy/tools/deps/docker_util.py
@@ -7,6 +7,7 @@
DEFAULT_WORKING_DIRECTORY = None
DEFAULT_NET = None
DEFAULT_MEMORY = None
+DEFAULT_VOLUMES_FROM = None
class DockerVolume(object):
@@ -55,6 +56,7 @@
tag=None,
docker_cmd=DEFAULT_DOCKER_COMMAND,
volumes=[],
+ volumes_from=DEFAULT_VOLUMES_FROM,
memory=DEFAULT_MEMORY,
env_directives=[],
working_directory=DEFAULT_WORKING_DIRECTORY,
@@ -75,6 +77,8 @@
command_parts.extend(["-e", env_directive])
for volume in volumes:
command_parts.extend(["-v", str(volume)])
+ if volumes_from:
+ command_parts.extend(["--volumes-from", str(volumes_from)])
if memory:
command_parts.extend(["-m", memory])
if name:
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.