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.baren@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.baren@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 <jmchilton@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.baren@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
>>> >
>>> >
>>> >
>>> > ___________________________________________________________
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>>
>>
>