Based on the screenshot you are calling the program correctly.

Can you tell me what version of Docker you are running and Galaxy you
are running? There have been a number of fixes in both programs over
the last six months to a year. Docker is known to consume a lot of
space in /var - it probably doesn't have much to do with Galaxy or
this tool right. It looks like you Docker command line does not
include -rm - which was added recently to have Docker dispose of
instances after it done with them. This might help with your /var
space issue - though in general Docker does use a lot a relatively
large amount of disk under /var - it is the nature of the technology
and many traditional HPC clusters for instance may allocate relatively
small /var partitions.

Upgrading Galaxy might also help the permission thing - I don't see a
'-u <uid>' argument in your command-line - which is another newer
default to help ensure the resulting files have the correct
permissions (especially when sudo is disabled - which it seems it is
in your configuration).

Hope this helps,

-John



On Mon, Jan 26, 2015 at 7:02 PM, Jeltje van Baren
<jeltje.van.ba...@gmail.com> wrote:
> Our sysadmin just notified me docker was taking up large amounts of space in
> /var/lib/docker/devicemapper/devicemapper/data
> and
> /var/lib/docker/devicemapper/devicemapper/metadata
>
> I noticed the following DEBUG message in paster.log:
>
> galaxy.jobs.runners.local DEBUG 2015-01-23 13:30:19,503 (12) executing job
> script:
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/galaxy_12.sh
> galaxy.jobs DEBUG 2015-01-23 13:30:19,552 (12) Persisting job destination
> (destination id: docker_local)
>
> Are these related? (the files I'm trying to concatenate are small text files
> so that's not it)
>
>
> On Mon, Jan 26, 2015 at 11:47 AM, Jeltje van Baren
> <jeltje.van.ba...@gmail.com> wrote:
>>
>> See attached for screenshot!
>>
>> Thanks for the links.
>>
>>
>>
>> On Mon, Jan 26, 2015 at 11:37 AM, John Chilton <jmchil...@gmail.com>
>> wrote:
>>>
>>> Can you send me a screenshot of the Tool form right before you hit
>>> submit. It is odd that two commands are executed barely differing at
>>> all. There were some recent UI changes and I want to make sure that
>>> you are passing two inputs once and not submitting one input twice in
>>> the newly named "batch mode"?
>>>
>>> container.sh is generated in command_factory.py using containers.py -
>>> here are some relevant links.
>>>
>>>
>>> https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/jobs/command_factory.py?at=default
>>>
>>> https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/tools/deps/containers.py?at=default
>>>
>>> https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/tools/deps/docker_util.py?at=default
>>>
>>> -John
>>>
>>>
>>> On Mon, Jan 26, 2015 at 2:17 PM, Jeltje van Baren
>>> <jeltje.van.ba...@gmail.com> wrote:
>>> > I'm still trying to debug this.
>>> >
>>> > How do I change the working directory? I can't seem to find out how all
>>> > those directory mounts get passed to docker - the catDocker.xml appears
>>> > to
>>> > generate a 'cat' command that I assume ends up in
>>> > ()/job_working_directory/000/12/container.sh
>>> > but I can't find where that's happening - container.sh isn't listed in
>>> > any
>>> > file under galaxy-dist.
>>> > job_conf.xml lists the directories that get passed as variables -
>>> > again,
>>> > when and where are those defined?
>>> >
>>> > Thanks,
>>> >
>>> > -Jeltje
>>> >
>>> >
>>> > On Fri, Jan 23, 2015 at 1:35 PM, Jeltje van Baren
>>> > <jeltje.van.ba...@gmail.com> wrote:
>>> >>
>>> >> I tried the second solution (setting everything to rw) and while I can
>>> >> confirm that the command is changed accordingly, the results are the
>>> >> same:
>>> >> Two empty output files and the same error message.
>>> >>
>>> >> Command from paster.log:
>>> >> docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist:rw
>>> >> -v
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:rw
>>> >> -v
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12:rw
>>> >> -v
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:rw
>>> >> -w
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12
>>> >> --net none busybox:ubuntu-14.04
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/container.sh;
>>> >> return_code=$?; if [ -f
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/working_file
>>> >> ] ; then cp
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/working_file
>>> >>
>>> >> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_19.dat
>>> >> ; fi; sh -c "exit $return_code"
>>> >>
>>> >> -Jeltje
>>> >>
>>> >> On Fri, Jan 23, 2015 at 12:24 PM, John Chilton <jmchil...@gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> My first thought is the bug mentioned here -
>>> >>>
>>> >>>
>>> >>> https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-November/020892.html
>>> >>> along with potential work arounds. Are you able to confirm that this
>>> >>> is or is not the problem at all?
>>> >>>
>>> >>> -John
>>> >>>
>>> >>> On Fri, Jan 23, 2015 at 2:37 PM, Jeltje van Baren
>>> >>> <jeltje.van.ba...@gmail.com> wrote:
>>> >>> > Hi,
>>> >>> >
>>> >>> > I'm following instructions at
>>> >>> > https://github.com/apetkau/galaxy-hackathon-2014.
>>> >>> >
>>> >>> > When I try to run the concatenate-datasets on two input files, two
>>> >>> > odd
>>> >>> > things happen. First, TWO nearly identical commands are generated
>>> >>> > in
>>> >>> > the
>>> >>> > History panel, only differing in their output filename. In
>>> >>> > paster.log,
>>> >>> > only
>>> >>> > the second one shows up. Second, the program fails, with this info
>>> >>> > in
>>> >>> > the
>>> >>> > History:
>>> >>> >
>>> >>> > An error occurred with this dataset:
>>> >>> > Galaxy slots passed through contain as 1
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/container.sh:
>>> >>> > line 2: can't create
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_14.dat
>>> >>> >
>>> >>> > This happens for both commands in the History panel, only the
>>> >>> > output
>>> >>> > filename in the other error is dataset_15.dat
>>> >>> >
>>> >>> > Oddly, the dataset_14.dat and dataset_15.dat are both created
>>> >>> > during
>>> >>> > this
>>> >>> > command, they just end up empty.
>>> >>> >
>>> >>> > Paster.log:
>>> >>> >
>>> >>> > galaxy.jobs.runners DEBUG 2015-01-23 11:08:35,973 (10) command is:
>>> >>> > docker
>>> >>> > inspect busybox:ubuntu-14.04 > /dev/null 2>&1
>>> >>> > [ $? -ne 0 ] && docker pull busybox:ubuntu-14.04 > /dev/null 2>&1
>>> >>> >
>>> >>> > docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist:ro
>>> >>> > -v
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:ro
>>> >>> > -v
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10:rw
>>> >>> > -v
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:rw
>>> >>> > -w
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10
>>> >>> > --net none busybox:ubuntu-14.04
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/container.sh;
>>> >>> > return_code=$?; if [ -f
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/working_file
>>> >>> > ] ; then cp
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/working_file
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_15.dat
>>> >>> > ; fi; sh -c "exit $return_code"
>>> >>> > galaxy.jobs.runners.local DEBUG 2015-01-23 11:08:36,040 (10)
>>> >>> > executing
>>> >>> > job
>>> >>> > script:
>>> >>> >
>>> >>> >
>>> >>> > /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/galaxy_10.sh
>>> >>> > galaxy.jobs DEBUG 2015-01-23 11:08:36,091 (10) Persisting job
>>> >>> > destination
>>> >>> > (destination id: docker_local)
>>> >>> >
>>> >>> >
>>> >>> > What could be happening here, and how do I fix it?
>>> >>> >
>>> >>> > Thanks,
>>> >>> >
>>> >>> > -Jeltje
>>> >>> >
>>> >>> >
>>> >>> >
>>> >>> > ___________________________________________________________
>>> >>> > Please keep all replies on the list by using "reply all"
>>> >>> > in your mail client.  To manage your subscriptions to this
>>> >>> > and other Galaxy lists, please use the interface at:
>>> >>> >   https://lists.galaxyproject.org/
>>> >>> >
>>> >>> > To search Galaxy mailing lists use the unified search at:
>>> >>> >   http://galaxyproject.org/search/mailinglists/
>>> >>
>>> >>
>>> >
>>
>>
>
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