2015-08-19 15:50 GMT+02:00 John Chilton <jmchil...@gmail.com>: > I don't know to be honest - a couple of things to verify. > > I wrote a bunch of debug stuff right away at the end of the e-mail and > you can try if I am wrong, but after I wrote I realized the problem. > You are not using sudo for running docker in your examples - this is > paused because sudo is waiting on a password and you don't have > passwordless sudo setup probably. > > I would just add <param id="docker_sudo">false</param> to your job > conf destination and this should work. >
Yes, this worked. Thanks! Regards > > The other stuff to try: > > Does the tool work without using Docker - if you just place test-io.sh > on Galaxy's PATH. If yes, I would set cleanup_job = never in > galaxy.ini and try again. Once it dies, grab this part of the command > line: > > sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:ro > -v > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:ro > -v > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:rw > -v > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:rw > -w > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2 > --net none --rm -u 1001 mikeleganaaranguren/busybox-galaxy-test-io:v1 > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh > > and try to debug the problem outside of Galaxy. Maybe using docker > logs for instance. If the logs don't reveal anything try dropping some > of the command-line arguments and see if that is the problem - e.g. " > --net none " or " -u 1001". > > -John > > On Tue, Aug 18, 2015 at 6:32 PM, Mikel Egaña Aranguren > <mikel.egana.arangu...@gmail.com> wrote: > > Hi; > > > > I'm trying to develop a Docker based tool, as suggested by a > peer-reviewer > > who might be reading this :P > > > > However, I'm having trouble with even the most basic setting, and I don't > > know what might be wrong, so any help will be much appreciated. I have > > developed a very simple docker image and corresponding Galaxy tool, so > that > > I get it working before starting with the actual tool, but when I > execute it > > through Galaxy it simply stays executing forever, instead of failing or > > terminating. > > > > My image simply executes a shell script that reads the content of a file > and > > concatenates a string to it. The image: > > > > FROM busybox:ubuntu-14.04 > > MAINTAINER Mikel Egaña Aranguren <mikel.egana.arangu...@gmail.com> > > > > RUN mkdir /sadi > > COPY test-io.sh /sadi/ > > RUN chmod a+x /sadi/test-io.sh > > ENV PATH $PATH:/sadi > > > > The test-io.sh script within the image: > > > > #!/bin/sh > > > > cat $1 > > echo "AAA" > > > > Invoking the container and executing the script through a normal shell > works > > fine: > > > > REPOSITORY TAG IMAGE ID > > CREATED VIRTUAL SIZE > > mikeleganaaranguren/busybox-galaxy-test-io v1 > > 9c2b8bdade1d 54 minutes ago 5.609 MB > > > > docker run -i -t mikeleganaaranguren/busybox-galaxy-test-io:v1 > > > > BusyBox v1.21.1 (Ubuntu 1:1.21.0-1ubuntu1) built-in shell (ash) > > Enter 'help' for a list of built-in commands. > > > > ~ # > > ~ # echo "BBB" > test > > ~ # test-io.sh test > > BBB > > AAA > > > > This is the tool file I'm using in Galaxy: > > > > <tool id="SADIBUSYBOX" name="SADIBUSYBOX"> > > <description>IO</description> > > <requirements> > > <container > > type="docker">mikeleganaaranguren/busybox-galaxy-test-io:v1</container> > > </requirements> > > <command> > > test-io.sh $input > $output > > </command> > > <inputs> > > <param name="input" type="data" label="Dataset"/> > > </inputs> > > <outputs> > > <data format="txt" name="output" /> > > </outputs> > > <help> > > </help> > > </tool> > > > > And my job_conf.xml: > > > > <?xml version="1.0"?> > > <!-- A sample job config that explicitly configures job running the way > it > > is configured by default (if there is no explicit config). --> > > <job_conf> > > <plugins> > > <plugin id="local" type="runner" > > load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> > > </plugins> > > <handlers> > > <handler id="main"/> > > </handlers> > > <destinations default="docker_local"> > > <destination id="local" runner="local"/> > > <destination id="docker_local" runner="local"> > > <param id="docker_enabled">true</param> > > </destination> > > </destinations> > > </job_conf> > > > > As I said, when I execute the tool in Galaxy, it simply executes > forever, it > > stays in a "yellow state", till I kill the Galaxy server. The log says: > > > > 127.0.0.1 - - [18/Aug/2015:19:08:00 +0200] "GET > > /tool_runner?tool_id=SADIBUSYBOX HTTP/1.1" 200 - "http://127.0.0.1:8080/ > " > > "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101 > > Firefox/40.0" > > galaxy.tools.actions INFO 2015-08-18 19:08:07,178 Handled output (77.825 > ms) > > galaxy.tools.actions INFO 2015-08-18 19:08:07,280 Verified access to > > datasets (12.387 ms) > > galaxy.tools.execute DEBUG 2015-08-18 19:08:07,307 Tool [SADIBUSYBOX] > > created job [2] (217.508 ms) > > 127.0.0.1 - - [18/Aug/2015:19:08:07 +0200] "POST /api/tools HTTP/1.1" > 200 - > > "http://127.0.0.1:8080/tool_runner?tool_id=SADIBUSYBOX"; "Mozilla/5.0 > (X11; > > Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:07 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > galaxy.jobs DEBUG 2015-08-18 19:08:07,714 (2) Working directory for job > is: > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2 > > galaxy.jobs.handler DEBUG 2015-08-18 19:08:07,721 (2) Dispatching to > local > > runner > > galaxy.jobs DEBUG 2015-08-18 19:08:07,839 (2) Persisting job destination > > (destination id: docker_local) > > galaxy.jobs.runners DEBUG 2015-08-18 19:08:07,849 Job [2] queued (128.176 > > ms) > > galaxy.jobs.handler INFO 2015-08-18 19:08:07,897 (2) Job dispatched > > galaxy.jobs.command_factory INFO 2015-08-18 19:08:08,163 Built script > > > [/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh] > > for tool > > > command[/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh] > > galaxy.jobs.runners DEBUG 2015-08-18 19:08:08,322 (2) command is: sudo > > docker inspect mikeleganaaranguren/busybox-galaxy-test-io:v1 > /dev/null > > 2>&1 > > [ $? -ne 0 ] && sudo docker pull > > mikeleganaaranguren/busybox-galaxy-test-io:v1 > /dev/null 2>&1 > > > > sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:ro > > -v > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:ro > > -v > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:rw > > -v > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:rw > > -w > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2 > > --net none --rm -u 1001 mikeleganaaranguren/busybox-galaxy-test-io:v1 > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh; > > return_code=$?; python > > > "/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/set_metadata_3aWBf9.py" > > "/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/tmp/tmpH2gy3X" > > > "/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/galaxy.json" > > > "/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_WxbKNP,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_p8UK91,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_wPm09U,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_irSo7t,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files/000/dataset_2.dat,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_1glVfb" > > 5242880; sh -c "exit $return_code" > > galaxy.jobs.runners.local DEBUG 2015-08-18 19:08:08,323 (2) executing job > > script: > > > /home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/galaxy_2.sh > > galaxy.jobs DEBUG 2015-08-18 19:08:08,375 (2) Persisting job destination > > (destination id: docker_local) > > 127.0.0.1 - - [18/Aug/2015:19:08:11 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:21 +0200] "GET > > /history/current_history_json HTTP/1.1" 200 - "http://127.0.0.1:8080/"; > > "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101 > > Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:21 +0200] "GET > > > /api/histories/f2db41e1fa331b3e/contents?dataset_details=ebfb8f50c6abde6d%2C33b43b4e7093c91f%2Ca799d38679e985db%2C5969b1f7201f12ae%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2C03501d7626bd192f%2C3f5830403180d620%2Ce85a3be143d5905b%2Cc9468fdb6dc5c5f1%2C2a56795cad3c7db3 > > HTTP/1.1" 200 - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; > Linux > > x86_64; rv:40.0) Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:25 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:29 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:33 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:38 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:42 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > 127.0.0.1 - - [18/Aug/2015:19:08:46 +0200] "GET > > /api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - > > "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:40.0) > > Gecko/20100101 Firefox/40.0" > > > > Thanks! > > > > -- > > Mikel Egaña Aranguren, Ph.D. > > > > http://mikeleganaaranguren.com > > > > > > > > ___________________________________________________________ > > 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/ > -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com
___________________________________________________________ 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/
