date:20161104

Re: [galaxy-dev] Errors when building Galaxy RNA-Seq Docker Image

2016-11-04 Thread Björn Grüning

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 758594

[galaxy-dev] Last Call for GMOD talks at PAG

2016-11-04 Thread Scott Cain

Time is short!

If you want to attend PAG  and would like to
present on a topic that would be of interest to the GMOD community, please
send an abstract or at least a descriptive title to h...@gmod.org. Types of
talks typically include updates on GMOD software projects, usage stories
for successful sites, proposals for new GMOD projects and descriptions of
plugins for existing GMOD software projects like Tripal
, JBrowse  and
Galaxy .

Please consider giving a talk and sharing your experience and ideas!
Scott

-- 

Scott Cain, Ph. D.   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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[galaxy-dev] Errors when building Galaxy RNA-Seq Docker Image

2016-11-04 Thread 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

Re: [galaxy-dev] filter options

2016-11-04 Thread Vincent Cahais

Sure, my combo-box is correctly filled with all options, but unfiltered.


 value, dbkey, name, path
 
 


Le 04/11/2016 à 13:42, Nicola Soranzo a écrit :
> Hi Vincent,
> have you defined the dbindel table in config/tool_data_table_conf.xml ?
>
> Cheers,
> Nicola
>
> On 04/11/16 08:09, Vincent Cahais wrote:
>> Dear All,
>>
>> I try to filter options for a param linked to a datatable.
>> I want to keep only options with the same dbkey as my input file. But i
>> cannot make it work.
>>
>> 
>> 
>>   
>>   
>>   
>> 
>>
>> ##dbindels
>> #   
>> hg38hg38Human
>> /data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf
>> mm10_1  mm10Mouse [All]
>> /data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz
>> mm10_2  mm10Mouse [129P2_OlaHsd]
>> /data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz 
>>
>>
>> Thank you for help,
>>
>> Vincent
>> ___
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>
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Re: [galaxy-dev] filter options

2016-11-04 Thread Nicola Soranzo


Hi Vincent,
have you defined the dbindel table in config/tool_data_table_conf.xml ?

Cheers,
Nicola

On 04/11/16 08:09, Vincent Cahais wrote:

Dear All,

I try to filter options for a param linked to a datatable.
I want to keep only options with the same dbkey as my input file. But i
cannot make it work.



  
  
  


##dbindels
#   
hg38hg38Human
/data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf
mm10_1  mm10Mouse [All]
/data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz
mm10_2  mm10Mouse [129P2_OlaHsd]
/data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz

Thank you for help,

Vincent
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Re: [galaxy-dev] conda management of tools dependent on python3

2016-11-04 Thread Nicola Soranzo


Hi Wolfgang,
I guess that the conda recipe should be updated to also specify

- python >=3

in the requirements.

Cheers,
Nicola

On 03/11/16 21:04, Wolfgang Maier wrote:

I'm not quite sure if I understand you correctly, but let's see.
The original tool wrapper stated

python3

as a dependency. This did not work with at runtime installation at all 
because conda cannot resolve python3 and the requirement got ignored 
by Galaxy. I changed the requirement tag now to:


python

and now Galaxy happily installs a __python@3.4 environment, but then 
it tries to set up a *new* environment for my package, which is still 
based on python2.7 and fails as before.
On the bioconda side, all the recipe does is to declare that it 
shouldn't be built under python2 using

skip: True # [py2k] in the build section of the recipe.


On 03.11.2016 21:36, Björn Grüning wrote:

Hi,

can you check the package? The package should have a dependency on
python3, if not the package seems to be broken :(

Ciao,
Bjoern

Am 03.11.2016 um 21:32 schrieb Wolfgang Maier:

Hi Björn,

Hmm, I guess I should have phrased my question more clearly. What I'm
trying to do is to get Galaxy to satisfy a missing tool dependency at
*tool runtime* using a bioconda package that is only available for
Python3. I am able to satisfy the dependency *manually* by running:

conda create --name __@
==https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), 


but when I let *Galaxy autoinstall* the package it will use python2.7
for the environment, then fail with:

Error: Unsatisfiable package specifications.

and a hint that  conflicts with python 2.7. So my question is:
is there any way to inform Galaxy that the dependency requires a conda
environment based on python3?

Best,
Wolfgang


On 28.10.2016 19:14, Björn Grüning wrote:

Hi Wolfgang,

can you describe step by step what you are trying to do?

A conda package ships it's own python version, you can see this in the
build-string py35_0 for example. So conda can handle all python 
version

independent of the python version of miniconda.

Cheers,
Bjoern


Dear all,

I'm still pretty new to conda tool dependencies management and 
there is

one thing I cannot find documented anywhere:
How can I let conda manage tool dependencies that involve python3?
If I let Galaxy install conda for me, it creates an environment with
python2, then if there is a tool dependency that has a conda package
built for only python3 I'm getting an error because of a conflict
between that package and python2 (not surprisingly), but AFAIU conda
environments are bound to one particular version of python (or is 
that

incorrect?).

Thanks for any help with this and best wishes,
Wolfgang
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[galaxy-dev] filter options

2016-11-04 Thread Vincent Cahais

Dear All,

I try to filter options for a param linked to a datatable.
I want to keep only options with the same dbkey as my input file. But i 
cannot make it work.



 
 
 


##dbindels
#   
hg38hg38Human 
/data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf
mm10_1  mm10Mouse [All] 
/data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz
mm10_2  mm10Mouse [129P2_OlaHsd] 
/data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz

Thank you for help,

Vincent
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Re: [galaxy-dev] Errors when building Galaxy RNA-Seq Docker Image

[galaxy-dev] Last Call for GMOD talks at PAG

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

Re: [galaxy-dev] filter options

Re: [galaxy-dev] filter options

Re: [galaxy-dev] conda management of tools dependent on python3

[galaxy-dev] filter options

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