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/
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