Errors when building Galaxy RNA-Seq Docker Image - galaxy-dev

4 Nov 2016


      I am trying to get this Docker image running:
https://github.com/bgruening/galaxy-rna-seq
If I let Docker download and start the container using this command:
docker run -d -p 8080:80 bgruening/galaxy-rna-seq
everything appears to work fine. However, if I clone the repo and try to build it myself like this:
docker build -t skelly/galaxy-rna-seq .
I get a load of errors. Here are a few:
...
...
Step 5 : RUN install-tools $GALAXY_ROOT/tools.yaml
---> Running in 78e96eb73823
Enable installation from the Test Tool Shed.
* Starting PostgreSQL 9.3 database server
   ...done.
starting Galaxy
./run.sh: 37: [: --daemon: unexpected operator
Activating virtualenv at /galaxy_venv
Requirement already satisfied (use --upgrade to upgrade): pip>=8.1 in /galaxy_venv/lib/python2.7/site-packages
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: 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. You can upgrade to a newer version of Python to solve this. 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:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarn....
  InsecurePlatformWarning
You are using pip version 8.1.2, however version 9.0.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
...
...
But I think the biggest problem is that the tools installation appears to fail:
...
...
Activating virtualenv at /galaxy_venv
Galaxy is running.
(1/10) Installing tool trim_galore from bgruening to section "Quality Control" at revision f1e71aeaa923 (TRT: 0:00:00.610888)
      Tool trim_galore installed successfully (in 0:01:46.048131) at revision f1e71aeaa923
(2/10) Installing tool suite_samtools_1_2 from devteam to section "SAM Tools" at revision 5b673ccc8747 (TRT: 0:01:46.874497)
      * Error installing a tool (after 0:00:05.381866 seconds)! Name: suite_samtools_1_2,owner: devteam, revision: 5b673ccc8747, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(3/10) Installing tool deseq2 from iuc to section "RNA-Seq" at revision 89bbd1dbf48d (TRT: 0:01:52.463056)
      * Error installing a tool (after 0:00:05.147542 seconds)! Name: deseq2,owner: iuc, revision: 89bbd1dbf48d, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(4/10) Installing tool deseq2 from iuc to section "RNA-Seq" at revision 8702e49e68b6 (TRT: 0:01:57.827642)
      * Error installing a tool (after 0:00:04.991533 seconds)! Name: deseq2,owner: iuc, revision: 8702e49e68b6, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(5/10) Installing tool htseq_count from lparsons to section "RNA-Seq" at revision a6dcb86af112 (TRT: 0:02:03.041254)
      * Error installing a tool (after 0:00:03.671927 seconds)! Name: htseq_count,owner: lparsons, revision: a6dcb86af112, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(6/10) Installing tool htseq_count from lparsons to section "RNA-Seq" at revision 6f920f33c5eb (TRT: 0:02:06.931447)
      Tool htseq_count installed successfully (in 0:04:57.743878) at revision 6f920f33c5eb
(7/10) Installing tool all_cufflinks_tool_suite from devteam to section "RNA-Seq" at revision d19a1295d99b (TRT: 0:07:04.933382)
      * Error installing a tool (after 0:00:06.615792 seconds)! Name: all_cufflinks_tool_suite,owner: devteam, revision: d19a1295d99b, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(8/10) Installing tool tophat2 from devteam to section "RNA-Seq" at revision 758594ed0364 (TRT: 0:07:11.768638)
      Tool tophat2 installed successfully (in 0:01:09.319561) at revision 758594ed0364
(9/10) Installing tool trinity from iuc to section "RNA-Seq" at revision 831abd20e690 (TRT: 0:08:21.314686)
      * Error installing a tool (after 0:00:08.002569 seconds)! Name: trinity,owner: iuc, revision: 831abd20e690, error: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
(10/10) Installing tool sailfish from bgruening to section "RNA-Seq" at revision 1b4ed566a41c (TRT: 0:08:29.534125)
      Tool sailfish installed successfully (in 0:00:02.506058) at revision 1b4ed566a41c
Installed tools (4): [('trim_galore', None), ('htseq_count', None), ('tophat2', None), ('sailfish', None)]
Skipped tools (0): []
Errored tools (6): [('suite_samtools_1_2', ''), ('deseq2', ''), ('deseq2', ''), ('htseq_count', ''), ('all_cufflinks_tool_suite', ''), ('trinity', '')]
All tools have been processed.
Total run time: 0:08:32.041138
The command '/bin/sh -c install-tools $GALAXY_ROOT/tools.yaml' returned a non-zero code: 1
Any ideas? I was hoping to use this as a base image and then add my own customizations.
Thanks
Stephen
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