bgruening / docker-galaxy-stable Goto Github PK

What would be the suggested way to fix this? Tool and dependency are coming from the toolshed, so technically the package_fastx_toolkit_0_0_13 would need to include the GD::Graph::bars perl module as a dependency.

job id: 45533
tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_clipping_histogram/cshl_fasta_clipping_histogram/1.0.0
tool version: 1.0.0
job pid or drm id: 1432
job tool version:

job command line:
fasta_clipping_histogram.pl /export/galaxy-central/database/files/057/dataset_57088.dat /export/galaxy-central/database/files/057/dataset_57089.dat

job stderr:
Can't locate GD/Graph/bars.pm in @inc (you may need to install the GD::Graph::bars module) (@inc contains: /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /galaxy-central/tool_deps/fastx_toolkit/0.0.13/devteam/package_fastx_toolkit_0_0_13/ec66ae4c269b/bin/fasta_clipping_histogram.pl line 21.
BEGIN failed--compilation aborted at /galaxy-central/tool_deps/fastx_toolkit/0.0.13/devteam/package_fastx_toolkit_0_0_13/ec66ae4c269b/bin/fasta_clipping_histogram.pl line 21.

While proftpd works for uploading files, passive ftp via it won't work since the passive ftp ports aren't exposed. The default range is 30000-40000, but of course exposing that many ports isn't feasible. One possible method around this would be to change proftpd.conf and set PassivePorts to a smaller range and then exposing that in the Dockerfile. Even exposing these from the command line is enough to get passive uploading/directory listing to work, though this requires modifying the proftpd configuration from within the container and then restarting the proftpd service...which is obviously less than ideal.

root@deep2: ~ $ docker run -t -i -v /docker_vm/:/export/ -v /data/:/data/ -p 8080:80 -p 21:21 bgruening/galaxy-stable /bin/bash
bash: warning: setlocale: LC_ALL: cannot change locale (en_US.utf-8)
root@fb26a2c66c74:/galaxy-central# echo $LC_ALL
en_US.utf-8
root@fb26a2c66c74:/galaxy-central# startup
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.utf-8)

This would prevent one from having to open yet another a port.

Might even be worth investigating replacing the node proxy with nginx plugin the way narrative does it.

using command docker run -d -p 8080:80 bgruening/galaxy-stable and accessing port 8080 of the target server gives:

It works!

This is the default web page for this server.

The web server software is running but no content has been added, yet.

Dumping the launch log via docker logs gives

galaxy.tools ERROR 2014-08-20 19:00:36,302 Error reading tool from path: mutation/visualize.xml

Full log at http://privatepaste.com/9373f62213

Perhaps unrelated, but attempting to build the dockerfile locally gives:

ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ensembl/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ncbi/builds.txt'
ERROR: Unable to read builds for site file /galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt

at step Step 60 : RUN service postgresql start && sleep 5 && python create_galaxy_user.py --user [email protected] --password admin --key admin

e.g. VOLUME ["/data"]

Hi,
How is it possible to include Apollo browser in Galaxy?

Thank you in advance.

Mic

I was trying to get access to the galaxy instance running in my docker. As this did not work I tried to start an interactive session:

docker run -i -t -p 8080:80 bgruening/galaxy-stable /bin/bash

but after

./run.sh

...
File "/galaxy-central/eggs/psycopg2-2.5.1_9.2.4_static-py2.7-linux-x86_64-ucs4.egg/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) could not connect to server: Connection refused
Is the server running on host "localhost" (::1) and accepting
TCP/IP connections on port 5432?
could not connect to server: Connection refused
Is the server running on host "localhost" (127.0.0.1) and accepting
TCP/IP connections on port 5432?

Hey Björn,

I just learned about Galaxy and I would like to introduce it to my QNIBTerminal; which provides an virtual HPC environment (logging, monitoring, inventory, slurm).

Looking at your Dockerfile I feel you kind of cheating, since you use Ansible to install galaxy...
If you don't mind me accusing you... :)
Is Galaxy that a pain in the a** to install, that you hide it; of is it just to not duplicate the installation as a first step?

Cheers and thanks for the head start
Christian

With the move of welcome.html to /etc/galaxy we added a new location to the nginx.conf

        location /root/welcome {
            alias /etc/galaxy;
            index welcome.html;
            gzip on;
            gzip_types text/plain text/xml text/javascript text/css application/x-javascript;
            expires 24h;
        }

Unfortunately, this seems to result in a cross origin request from localhost:8080. If we run the container on port 80 everything works fine. The error on any other port is:

ncaught SecurityError: Failed to read the 'contentDocument' property from 'HTMLIFrameElement': Blocked a frame with origin "http://localhost:8080" from accessing a frame with origin "null".  The frame requesting access has a protocol of "http", the frame being accessed has a protocol of "data". Protocols must match.

I guess we need some nginx magic here.

It would be nice to integrate slurm or condor into docker. Condor has some nice features to communicate with other SGE/OGE based systems. So we currently prefer (slightly) Condor.

Hello,
I have tried to start docker with the following command:

$ sudo docker run -p 8080:80 -p 8800:8800 --privileged=true -v /home/lorencm/galaxy_storage/:/export/ -e "[email protected]" -e "GALAXY_CONFIG_BRAND='My own Galaxy flavour'" bgruening/galaxy-stable

However, I recieved the folliwng error massage on Cent OS 6.6 and docker version 1.6.2, build 7c8fca2/1.6.2:

Enable Galaxy Interactive Environments.
mkdir: cannot create directory ‘/sys/fs/cgroup’: No such file or directory
mount: mount point /sys/fs/cgroup does not exist
Could not make a tmpfs mount. Did you use -privileged?
/usr/lib/python2.7/dist-packages/supervisor/options.py:295: UserWarning: Supervisord is running as root and it is searching for its configuration file in default locations (including its current working directory); you probably want to specify a "-c" argument specifying an absolute path to a configuration file for improved security.
  'Supervisord is running as root and it is searching '

Does the above error caussing that my history menu does not contain e.g. "import from file"?
My Current History

• Resume Paused Jobs
• Unhide Hidden Datasets
• Delete Hidden Datasets
• Show Structure
• Export Citations
• Export to File

Thank you in advance.

Mic

Since the servers.ini is appended to galaxy.ini, it's not required anymore and doesn't need to be part of the persistent config files that get copied to the host.

I installed 10-15 tools, and 2 managers including Reference genome fetch.
When refrechingGalaxy main page, each time tools randomly showing up and dissaperring.
Also happend in Data managers. When refreshed I see 1 of the 2 but never all of it (randomly also).

More over when clicking on some Data manager randomly I see it is missing in a red label at the top, and sometimes it loads properly.
When I start to fetch human genome in history it drops error - This tool was disabled before the job completed.

I started the Galaxy just as stated:
docker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
and installed tools.

I'm confused where can be the problem

Hi
in the last days everytime I want to restart Galaxy, after I install some tools I got error from galaxy_web:
sudo docker exec f187b0f37822 supervisorctl restart galaxy:
galaxy_nodejs_proxy: stopped
handler0: stopped
handler1: stopped
galaxy_web: stopped
galaxy_nodejs_proxy: started
galaxy_web: ERROR (abnormal termination)
handler0: started
handler1: started

If than If stop the container, restart docker service and start new Galaxy container, it is ok?

It is very useful to use galaxy-docker as means to deploy Galaxy in dev, test and production environment. However, current galaxy-docker-stable image does not allow to modify Galaxy buildtime variables, like GALAXY_HOME, GALAXY_GID and GALAXY_UID. In order for the container to be useful in this process, there needs to be a way to change at least those variables.

This issue is created based on the galaxy-dev mailing list discussion "Externalizing Galaxy config in docker-galaxy-stable":
http://dev.list.galaxyproject.org/Externalizing-Galaxy-config-in-docker-galaxy-stable-td4667648.html

Addressing all of these probably requires changes to Galaxy.

• database/tmp/upload_store - should be placed somewhere else, maybe just /tmp/galaxy_upload.
• ADD ./servers.ini /galaxy-central/config/servers.ini (#42)
• ADD ./job_conf.xml /galaxy-central/config/job_conf.xml (#42)
• RUN cd /galaxy-central/lib/galaxy/web/proxy/js && npm install
• Welcome `ADD GalaxyDocker.png /galaxy-central/static/welcome/GalaxyDocker.png
• ADD welcome.html /galaxy-central/static/welcome.html`

Hi, I tried to run this docker image as below show, but I am not able to connect from a browser to http://127.0.0.1:8080/ and http://127.0.0.1:9191/.

    $ sudo docker run -p 8080:80 bgruening/galaxy-stable
umount: /var/lib/docker: must be superuser to umount
tmpfs on /proc/kcore type tmpfs (rw,nosuid,seclabel,mode=755)
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
/usr/lib/python2.7/dist-packages/supervisor/options.py:295: UserWarning: Supervisord is running as root and it is searching for its configuration file in default locations (including its current working directory); you probably want to specify a "-c" argument specifying an absolute path to a configuration file for improved security.
  'Supervisord is running as root and it is searching '
Starting ProFTP
proftpd: started
Starting Galaxy reports webapp
reports: started
Starting nodejs
galaxy:galaxy_nodejs_proxy: ERROR (abnormal termination)

?.

galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,888 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,892 Enabling 'remote_files' API controller, class: RemoteFilesAPIController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,894 Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,894 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,895 Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,896 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,897 Enabling 'metrics' API controller, class: MetricsController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,898 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,899 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,901 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,902 Enabling 'tool_data' API controller, class: ToolData
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,903 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,903 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,904 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,905 Enabling 'pages' API controller, class: PagesController
galaxy.web.framework.base DEBUG 2015-08-08 08:13:41,908 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,317 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,318 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,323 Enabling 'error' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,324 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,324 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-08-08 08:13:42,325 Enabling 'Request ID' middleware
Sat Aug  8 08:13:42 2015 - WSGI app 0 (mountpoint='') ready in 58 seconds on interpreter 0x223ddc0 pid: 41 (default app)
Sat Aug  8 08:13:42 2015 - *** uWSGI is running in multiple interpreter mode ***
Sat Aug  8 08:13:42 2015 - spawned uWSGI master process (pid: 41)
Sat Aug  8 08:13:42 2015 - spawned uWSGI worker 1 (pid: 191, cores: 4)
Sat Aug  8 08:13:42 2015 - spawned uWSGI worker 2 (pid: 192, cores: 4)
Sat Aug  8 08:13:42 2015 - *** Stats server enabled on 127.0.0.1:9191 fd: 12 ***
galaxy.queue_worker INFO 2015-08-08 08:13:42,329 Binding and starting galaxy control worker for main.1
galaxy.queue_worker INFO 2015-08-08 08:13:42,331 Binding and starting galaxy control worker for main.2

My Docker version is 1.6.2, build 7c8fca2/1.6.2.

Thank you in advance,

Mic

The seems to be in /galaxy-central and not in the config directory, so it's not exported to the host system.

Hi Björn

I am currently running the development version op the docker image for Galaxy. When I install a tool or data manager, they are not listed in the list of useable tools/data managers. However, when I refresh the page they appear (although the installed tools aren't is the right section). On a subsequent refresh, everything is gone again, and so on.
All installed tools do show up in the admin interface under "manage installed tools".

When trying to use and installed data manager/tool I get the following error box:

Invalid Data Manager (toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager/fetch_genome_all_fasta/0.0.1) was requested

Tool 'toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.3.1' does not exist.

I checked the /export folder for the mentioned tools, and the referenced folders do not exist. So it seems something goes wrong during the installation process, although the tools are marked as "installed" in the database.

Any ideas?

Matthias

Add on option to migrate the Galaxy database via an ENV variable or a special entry point. This should make it easier to migrate from one galaxy-docker version to a new one.

Hi,

I will give a small presentation at the upcoming Galaxy Community Conference and BOSC about this project. Please feel free to add anything what you think is important for users and developers and should be added!

Thanks,
Bjoern

What do I need to change in order for slurm to use the 64 cores my server has? How do I allow each user to run e.g. 5 concurrent jobs, with a max of 10 concurrent jobs overall and max. 4 cores per job?

I tried changing the job_conf.xml accordingly, but nothing changed, it still just ran one job at a time.

<?xml version="1.0"?>
<job_conf>
    <plugins workers="10">
        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
        </plugin>
    </plugins>
    <handlers default="handlers">
        <handler id="handler0" tags="handlers"/>
        <handler id="handler1" tags="handlers"/>
    </handlers>
    <destinations default="cluster">
        <destination id="cluster" runner="slurm">
            <!-- <param id="docker_enabled">true</param> -->
            <param id="docker_sudo">false</param>
            <param id="docker_volumes_from">galaxy</param>
            <param id="local_slots">4</param>
        </destination>
    </destinations>
    <limits>
        <!-- Certain limits can be defined. -->
        <limit type="registered_user_concurrent_jobs">5</limit>
        <limit type="unregistered_user_concurrent_jobs">1</limit>
        <limit type="job_walltime">72:00:00</limit>
        <limit type="output_size">536870912000</limit>
    </limits>
</job_conf>

The symlinks of those directories from /galaxy-central to /export are not made. Maybe because the source directories do not exist when the server is started?

See comments in #37 (comment).

Should be done before dev is merged into stable.

We should remove postgresql and proftp from the main image and base this on the original image. Orchestration can be done fig.

Not sure how this can work with the new ansible rules.

Similar to galaxyproject/usegalaxy-playbook#9 we should migrate to ansible-galaxy-tools for all tool installations.

• make sure old installation will still work (keep our script)
• make use of ansible-galaxy-tools
• figure out how to install tools into multiple categories at a time
• add Galaxy API to create new categories

@afgane @jmchilton @natefoo Any opinion on integrating this role here vs. getting it into ansible-galaxy-extras?

We need some best practice guideline how to:

• upgrade images
• use slurm to submit to host scheduler

Allow runtime specified environment variables to control:

• Whether optional components are enabled (node proxy, reports, proftpd...)
• The number of job handler processes.
• The number of uwsgi processes (fixed in #113).

Hi,
There is a good chance the following is due to my own misunderstanding of how the FTP server which is shipped with Galaxy is configured, but here it is. I am testing the FTP connection with a vanilla Galaxy container and cannot get past a '530 Login incorrect' error. I checked that the container's port 8021 was mapped to localhost:21, so I don't think the problem is there.

Something that would help me is: what is the default username and password for a FTP user? I tried 'galaxy', 'galaxy@localhost', '[email protected]', and I can't get any to work with any combination of 'galaxy' or 'admin' as password.

Best,
Aurelien

From Kyle:

Trying to use the tool download function, ie /api/tools/tool_name/download
and I get a 404.

Example:

curl http://128.114.61.142:9999/api/tools/MuSE/download?key=admin
<html>
<head><title>404 Not Found</title></head>
<body bgcolor="white">
<center><h1>404 Not Found</h1></center>
<hr><center>nginx/1.4.6 (Ubuntu)</center>
</body>
</html>

The Galaxy log does just fine:

[pid: 158|app: 0|req: 295/295] 76.126.58.122 () {32 vars in 420 bytes} [Thu Mar 26 06:45:50 2015] GET /api/tools/MuSE/download?key=admin => generated 0 bytes in 15 msecs (HTTP/1.1 200) 5 headers in 269 bytes (1 switches on core 2)

I have started an upload job for a files 11G each and I got error:

Unable to fetch http://10.98.33.151/web-uploads/R1_trimmed.fq [Errno 28] No space left on device

But I gave 23TB free on the machine :) So probably some file size limitation or?

Me again, I try to build the image and got this:

Step 16 : RUN ansible-playbook /tmp/ansible/provision.yml     --extra-vars galaxy_user_name=$GALAXY_USER     --extra-vars galaxy_config_file=$GALAXY_CONFIG_FILE     --extra-vars galaxy_config_dir=$GALAXY_CONFIG_DIR     --extra-vars galaxy_job_conf_path=$GALAXY_CONFIG_JOB_CONFIG_FILE     --extra-vars galaxy_job_metrics_conf_path=$GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE     --tags=galaxyextras -c local &&     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Running in 0b24ad6cfa38
ERROR: found role at /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras, but cannot find /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/tasks/main or /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/handlers/main or /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/vars/main or /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/defaults/main or /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/meta/main or /tmp/ansible/roles/galaxyprojectdotorg.galaxyextras/library
2015/05/05 16:37:34 The command [/bin/sh -c ansible-playbook /tmp/ansible/provision.yml     --extra-vars galaxy_user_name=$GALAXY_USER     --extra-vars galaxy_config_file=$GALAXY_CONFIG_FILE     --extra-vars galaxy_config_dir=$GALAXY_CONFIG_DIR     --extra-vars galaxy_job_conf_path=$GALAXY_CONFIG_JOB_CONFIG_FILE     --extra-vars galaxy_job_metrics_conf_path=$GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE     --tags=galaxyextras -c local &&     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*] returned a non-zero code: 1

IMO, the [group:galaxy] should contain all galaxy processes, so users restarting galaxy can simply supervisorctl restart galaxy:. This is in reference to today's discussion on IRC.

This would look like:

[group:galaxy]
programs=handler,galaxy_uwsgi

sorry, would PR but other things going on

Hi

Are there any plans for torque support through the docker container? Or is this already possible? If so, how would I go about to get this to work?

Thx!
Matthias

Move all configuration files out of that directory - update commands to point to these new configuration files.

I think this would provide a clearer upgrade path over time for people running these images but I think the more important feature of it would be that could expose a local copy of galaxy-central using the -v option and then use this same container for automated testing during galaxy-central development.

Nate has been doing a lot of work to make this easier (e.g. https://bitbucket.org/galaxy/galaxy-central/pull-request/495/clean-up-the-root-directory-and-rename). I think on the Galaxy side what would help even more is if everything in universe_wsgi.ini/galaxy.ini could be overridden with environment variables. Then ENV could be used to configure Galaxy and users could override these or other options at runtime with -e.

Hi Björn,

When trying to create a custom flavour of your galaxy docker appliance, I keep getting errors from the PostgreSQL server wile building the image.

OperationalError: (psycopg2.OperationalError) FATAL:  the database system is starting up

The code is my Dockerfile is as follows

RUN install-repository \
# Install Data Managers
    "--url $TOOLSHED -a $GALAXY_CONFIG_MASTER_API_KEY -o devteam -n data_manager_bowtie2_index_builder --repository-deps --tool-deps"

which looks correct to me.

Any idea what I could do about this? When I run docker locally and try to build the image on my personal system it works (sometimes), but when I try to build it on our cloud infrastructure I keep on getting this error.

PS: any plans to update the image to Galaxy v15.07?

Thanks
Matthias

From @bgruening - "I can transfer data to proftp but Galaxy is not able to pick them up. This is because the permissions of the user FTP data is wrong."

I am not sure what the fix here is - this problem is the result of running Galaxy as a non-root user right (not the ansible changes)? Should we ensure /export/galaxy-central/database/ftp exists in export_user_files.py and owned by the Galaxy user? Also is /export the right place for this?

For the time being we will stick to sha2 to encrypt user passwords. If we migrate to a newer base image, with a more recent proftpd version we should switch over to use PBKDF2.

For now we have: pbkdf2 = False in galaxy.ini and User.use_pbkdf2 = False in create_galaxy_user.py

/galaxy-central/tools/extract/extract_genomic_dna.py issues a call to faToTwoBit. Since the wrapper is inside the container, any change would not be persisent.

It seems that gnuplot (or at least the python interface to it) isn't getting installed by default. Consequently, things like "Graph/Display Data"->"bar char" don't work. One also can't install the gnuplot-py because it apparently requires numpy but doesn't list that as a requirement (that seems like a toolshed oversight).

Hello,
I am getting the bellow warning:

/usr/lib/python2.7/dist-packages/supervisor/options.py:295: UserWarning: Supervisord is running as root and it is searching for its configuration file in default locations (including its current working directory); you probably want to specify a "-c" argument specifying an absolute path to a configuration file for improved security.
  'Supervisord is running as root and it is searching '

with the following error:

sudo docker run -p 8080:80 -p 8800:8800 \
--privileged=true -e DOCKER_PARENT=True \
-v /var/run/docker.sock:/var/run/docker.sock \
-v /home/lorencm/galaxy_storage/:/export/ \
-e "[email protected]" \
bgruening/galaxy-stable 

What did I do wrong?

mic

I noticed that quite some tools from the toolshed expect zlib (headers) to be installed (even if they bring their own dependencies like vcftools from devteam).

Hi, by any chance are there any docker images which uses usegalaxy-playbok?

... , indicating that Galaxy needs a few seconds to start. Galaxy logo, liks to wiki, videos and biostars.

See comment galaxyproject/ansible-galaxy-extras#4 (comment) - I think it would be more convenient for both personal instances and institutional/public servers. Not immediately obvious how to do this though since it requires some nginx magic to conditionally password protect that route.

NOTE: I am using boot2docker v1.6.1 on OSX 10.9.5.

Command: docker run -p 8080:80 -v /Users/lparsons/galaxy_storage/:/export/ bgruening/galaxy-stable

Result: /Users/lparsons/galaxy_storage/ is created on my OSX machine and populated with galaxy_central, postgresql, shed_tools and var directories. However, I then run into the following error:

==> /home/galaxy/uwsgi.log <==
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 51, in app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "lib/galaxy/app.py", line 38, in __init__
    self.config.check()
  File "lib/galaxy/config.py", line 618, in check
    self._ensure_directory( path )
  File "lib/galaxy/config.py", line 599, in _ensure_directory
    raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
ConfigurationError: Unable to create missing directory: /export/galaxy-central/database/files
[Errno 13] Permission denied: '/export/galaxy-central/database'

Various other logs report errors due to the directory /export/galaxy-central/database/files not existing.

I've attempted to manually create this directory, but then I get similar errors about other directories and I wasn't ever able to get things to startup.

docker-galaxy-stable docker restart will lose all files under galaxy-central/config, and when add lots of tools , it will appear differently on left tool panel.