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.aranguren@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!