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"
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>> >
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>>
>
>
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