Question: Docker hangs when creating new Galaxy container
0
gravatar for steve
22 months ago by
steve30
NYC
steve30 wrote:

Following the instructions here, this is my Dockerfile:

# Galaxy - Test
#
# VERSION       0.01

FROM bgruening/galaxy-stable

ENV GALAXY_CONFIG_BRAND MyTestGalaxy
ENV GALAXY_CONFIG_ENABLE_BETA_TOOL_COMMAND_ISOLATION True
ENV GALAXY_CONFIG_SERVE_XSS_VULNERABLE_MIMETYPES True

#RUN add-tool-shed --url 'https://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'

# Install deepTools
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name suite_deeptools --panel-section-name deepTools"

# Install bowtie2, fastqc
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name bowtie2 --panel-section-id solexa_tools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name data_manager_bowtie2_index_builder" \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name data_manager_fetch_genome_dbkeys_all_fasta" \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name fastqc --panel-section-id NGS_QC"

# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
EXPOSE :80
EXPOSE :21
EXPOSE :8800

# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]

I am running Docker version 1.12;

$ docker --version
Docker version 1.12.0, build 8eab29e

I am trying to create the Docker container with this command:

$ docker build .

It gets up to this point:

...
...
Step 5 : RUN install-repository     "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name suite_deeptools --panel-section-name deepTools"
 ---> Running in 0b852ebfd3cf
 * Starting PostgreSQL 9.3 database server
   ...done.
Activating virtualenv at /galaxy_venv
Ignoring indexes: https://pypi.python.org/simple
Collecting pip==8.0.2+gx2
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB)
Installing collected packages: pip
  Found existing installation: pip 1.5.4
    Uninstalling pip-1.5.4:
      Successfully uninstalled pip-1.5.4
Successfully installed pip-8.0.2+gx2
Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /galaxy_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
...
...
...
Requirement already satisfied (use --upgrade to upgrade): PasteScript in /galaxy_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade): pyparsing>=2.0.1 in /galaxy_venv/lib/python2.7/site-packages (from svgwrite==1.1.6->-r requirements.txt (line 57))
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in /galaxy_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1))
Requirement already satisfied (use --upgrade to upgrade): drmaa in /galaxy_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2))
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Activating virtualenv at /galaxy_venv
Galaxy is running.
Processing:      --url https://toolshed.g2.bx.psu.edu/ -o bgruening --name suite_deeptools --panel-section-name deepTools

^^^ It gets stuck at this point and hangs indefinitely.

Any idea what is going on?

docker • 686 views
ADD COMMENTlink written 22 months ago by steve30
1
gravatar for Devon Ryan
22 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

If you want to use the deepTools container then you can just docker pull it from quay.io or dockerhub. Otherwise, you end up needing to install all of the dependencies, which will take a good bit of time (this is the "hanging" that you're seeing).

ADD COMMENTlink written 22 months ago by Devon Ryan1.9k

OK, I saw that listed in the original deepTools template Dockerfile but did not realize it was needed for generating a template. Also could not tell that the 'hanging' was the system actually running and not breaking. Thanks

ADD REPLYlink written 22 months ago by steve30

I also think it was still installing, it can take hours. The newest version do use conda packages and it should be finished in minutes, but for this you need to use the latest Galaxy version and the yaml based tool definitions.

ADD REPLYlink written 22 months ago by Bjoern Gruening5.1k

Yes you and Devon were right, it was still installing. I tried it again and left it run for a while and it did eventually finish. Thanks

ADD REPLYlink modified 22 months ago • written 22 months ago by steve30
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