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.bri...@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.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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