[galaxy-dev] virtualenv, jpype, and tool_dependencies.xml

[Michael E. Cotterell]

I'm trying to setup a virtualenv with JPype via tool_dependencies.xml. I've 
verified that JPype is available from PyPI via pip, however, when Galaxy tries 
to install the dependency, it's not finding a distribution.  

JPype 0.5.4.2 https://pypi.python.org/pypi/JPype

Here is the  snippet from my tool_dependies.xml file:




JPype==0.5.4.2



In order to install JPype, you must agree to the Apache License, Version 
2.0, January 2004 (http://www.apache.org/licenses/)




Here is the error that I get when trying to install the dependency:

New python executable in 
/home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/venv/bin/python
Installing setuptoolsdone.
Installing pip...done.
Downloading/unpacking JPype==0.5.4.2 (from -r 
/home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt
 (line 1))
Could not find any downloads that satisfy the requirement JPype==0.5.4.2 
(from -r 
/home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt
 (line 1))
No distributions at all found for JPype==0.5.4.2 (from -r 
/home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt
 (line 1))
Storing complete log in /home/mepcotterell/.pip/pip.log



Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
Faculty Liaison, CS Graduate Student Association, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/


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Re: [galaxy-dev] VirtualEnv

[Nate Coraor]

On Feb 6, 2013, at 11:04 AM, Thyssen, Gregory - ARS wrote:

> Hello
> Everything seems to be working on my local Galaxy
> I was talking to my IT guy who did the initial installation and he said that 
> virtualenv may not have been loaded.
> When he did
> % yum install python-virtualenv.noarch
> He got a not found error.
>  
> He did install mercurial and then completed the Install instructions from
> www.biocodershub.net/community/guest-post-notes-on-installing-galaxy/
>  
> What should we do at this point?
> Is VirtualEnv dispensible?
> What should I expect to be broken?
> Whats the fix?

Hi Greg,

virtualenv is not required, it just prevents site packages (extra modules not 
installed with the default python interpreter) from interfering with Galaxy's 
internally managed dependencies.  You can also install virtualenv using pip, 
easy_install, setup.py, or by just downloading virtualenv.py and running it 
directly.

http://pypi.python.org/pypi/virtualenv

--nate

>  
> Thank you,
>  
> Gregory Thyssen, PhD
> Molecular Biologist
> Cotton Fiber Bioscience
> USDA-ARS-Southern Regional Research Center
> 1100 Robert E Lee Blvd
> New Orleans, LA 70124
> gregory.thys...@ars.usda.gov
> 504-286-4280
>  
>  
> 
> 
> 
> 
> This electronic message contains information generated by the USDA solely for 
> the intended recipients. Any unauthorized interception of this message or the 
> use or disclosure of the information it contains may violate the law and 
> subject the violator to civil or criminal penalties. If you believe you have 
> received this message in error, please notify the sender and delete the email 
> immediately. ___
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[galaxy-dev] VirtualEnv

[Thyssen, Gregory - ARS]

Hello
Everything seems to be working on my local Galaxy
I was talking to my IT guy who did the initial installation and he said that 
virtualenv may not have been loaded.
When he did
% yum install python-virtualenv.noarch
He got a not found error.

He did install mercurial and then completed the Install instructions from
www.biocodershub.net/community/guest-post-notes-on-installing-galaxy/

What should we do at this point?
Is VirtualEnv dispensible?
What should I expect to be broken?
Whats the fix?

Thank you,

Gregory Thyssen, PhD
Molecular Biologist
Cotton Fiber Bioscience
USDA-ARS-Southern Regional Research Center
1100 Robert E Lee Blvd
New Orleans, LA 70124
gregory.thys...@ars.usda.gov
504-286-4280






This electronic message contains information generated by the USDA solely for 
the intended recipients. Any unauthorized interception of this message or the 
use or disclosure of the information it contains may violate the law and 
subject the violator to civil or criminal penalties. If you believe you have 
received this message in error, please notify the sender and delete the email 
immediately.
___
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