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Errors when building Galaxy RNA-Seq Docker Image

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Errors when building Galaxy RNA-Seq Docker Image

Stephen Kelly

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#insecureplatformwarning.

  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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Re: Errors when building Galaxy RNA-Seq Docker Image

Björn Grüning-3
Hi Stephen,

this was due to a downtime of the TS as far as I can tell.
But I took the opportunity to update the tools and include conda
dependencies. Please pull again and rebuild. It works for me know.

Thanks and let me know if anything is missing!
Cheers,
Bjoern

Am 04.11.2016 um 19:17 schrieb Stephen Kelly:

> 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#insecureplatformwarning.
>
>   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
>
>  
>
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of
> the intended recipient(s) and may contain information that is
> proprietary, confidential, and exempt from disclosure under applicable
> law. Any unauthorized review, use, disclosure, or distribution is
> prohibited. If you have received this email in error please notify the
> sender by return email and delete the original message. Please note, the
> recipient should check this email and any attachments for the presence
> of viruses. The organization accepts no liability for any damage caused
> by any virus transmitted by this email.
> =================================
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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:
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