1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82ce88b096ff/ Changeset: 82ce88b096ff User: dannon Date: 2014-10-13 15:23:42+00:00 Summary: Merged in kellrott/galaxy-farm/docker-work (pull request #525) Adding 'set user' flag to docker calls Affected #: 3 files diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -196,7 +196,8 @@ adding the '\-\-rm' flag to the command line, the container will be removed automatically after the program is complete. --> - <!-- <param id="docker_auto_rm">false</param> --> + <!-- <param id="docker_auto_rm">true</param> --> + <!-- <param id="docker_set_user">true</param> --><!-- Following command can be used to tweak docker command. --><!-- <param id="docker_cmd">/usr/local/custom_docker/docker</param> --><!-- Following can be used to connect to docke server in different diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -243,7 +243,8 @@ env_directives=env_directives, working_directory=working_directory, net=prop("net", "none"), # By default, docker instance has networking disabled - auto_rm=prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE), + auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), + set_user=asbool(prop("set_user", docker_util.DEFAULT_SET_USER)), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -10,6 +10,7 @@ DEFAULT_MEMORY = None DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True +DEFAULT_SET_USER = True class DockerVolume(object): @@ -119,6 +120,7 @@ sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, auto_rm=DEFAULT_AUTO_REMOVE, + set_user=DEFAULT_SET_USER, host=DEFAULT_HOST, ): command_parts = __docker_prefix( @@ -146,6 +148,8 @@ command_parts.extend(["--net", net]) if auto_rm: command_parts.append("--rm") + if set_user: + command_parts.extend(["-u", str(os.geteuid())]) full_image = image if tag: full_image = "%s:%s" % (full_image, tag) 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.