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
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?
On Fri, Jan 23, 2015 at 1:35 PM, Jeltje van Baren <
> 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=$GALAXY_SLOTS" -v
> --net none busybox:ubuntu-14.04
> return_code=$?; if [ -f
> ] ; then cp
> ; fi; sh -c "exit $return_code"
> On Fri, Jan 23, 2015 at 12:24 PM, John Chilton <jmchil...@gmail.com>
>> My first thought is the bug mentioned here -
>> along with potential work arounds. Are you able to confirm that this
>> is or is not the problem at all?
>> 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,
>> > the second one shows up. Second, the program fails, with this info in
>> > History:
>> > An error occurred with this dataset:
>> > Galaxy slots passed through contain as 1
>> > line 2: can't create
>> > 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
>> > command, they just end up empty.
>> > Paster.log:
>> > galaxy.jobs.runners DEBUG 2015-01-23 11:08:35,973 (10) command is:
>> > 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
>> > -v
>> > -v
>> > -v
>> > -w
>> > --net none busybox:ubuntu-14.04
>> > return_code=$?; if [ -f
>> > ] ; then cp
>> > ; fi; sh -c "exit $return_code"
>> > galaxy.jobs.runners.local DEBUG 2015-01-23 11:08:36,040 (10) executing
>> > script:
>> > galaxy.jobs DEBUG 2015-01-23 11:08:36,091 (10) Persisting job
>> > (destination id: docker_local)
>> > What could be happening here, and how do I fix it?
>> > Thanks,
>> > -Jeltje
>> > ___________________________________________________________
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