Hi Peter, 

Thank you so much. 

I'll see what I can figure out with these pull requests. I'm still quite inexperienced with these types of files. This is probably a good opportunity to learn some new code/structures. 

If I can't manage to figure it out, I hope there's another variant caller with different dependencies I can use for my project. 

Best, 

Jen 

On 9 Jan 2017 4:06 p.m., "Peter Briggs" <peter.briggs@manchester.ac.uk> wrote:

Hello Jennifer

I came across the same problem with the naive variant caller at the end of last year, when trying to upgrade our local Galaxy instance.

As you describe, the issue is actually with the two dependency packages:

-- package_pybamparser_0_0_1
-- package_pybamtools_0_0_2

I think I found the same solution as Nikolaos to the underlying problem (i.e. the setup.py files in these two packages are no longer compatible with the newer versions of the Python 'setuptools'), but I didn't have time to follow it up then.

I've now submitted pull requests with my attempted fixes on the Bitbucket repositories which hold the source code for the dependencies (URLs below), so at least you can see how I've tried to address the problem. However I don't know of an easy way to apply these changes inside the Galaxy context - my hope is that the tool maintainer (Daniel Blankenberg, cc'ed) will take a look and update the dependencies on the toolshed.

Not sure if this helps - maybe someone else on this list has a way to apply the patches directly?

Best wishes

Peter

Pull request URLs:

-- https://bitbucket.org/dan/pybamtools/pull-requests/1/
-- https://bitbucket.org/dan/pybamparser/pull-requests/3/

On 06/01/17 14:50, Jennifer Hsieh wrote:

Hi,
I've installed a local instance of Galaxy (on Ubuntu 16.04, python
2.7.12) and have run in to this exact problem
(posted by Nikolaos
Tur https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg03955.html)
while trying to add naive_variant_caller tool.
Naive_variant_caller can't install because these two dependency packages
can't be installed.
I basically get exactly the same error message that ends with "IOError:
Could not build the egg."

Unfortunately I'm very new to both Galaxy and Python (Taking Coursera
Galaxy course at the moment) and I don't really understand the solution
Nikolaos described about modifying the setup.py to use "setuptools"
instead of "distribute". I don't even know where to find setup.py...

Can anyone help me with step-by-step details as to how to solve this
dependency problem?

Much Thanks!
--
Jennifer Hsieh
PhD Neuroscience (student)
Department of Psychiatry and Mental Health
University of Cape Town
Tell: +27 21 447 3157
Cell: +27 74 841 4761

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--
Peter Briggs peter.briggs@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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