Hi all,

These packages should now install correctly from the toolshed with Peter’s PR. 
Please let me know if you encounter additional issues.



Thanks for using Galaxy,

Dan

> On Jan 31, 2017, at 10:47 PM, Jennifer Hsieh <humbleambit...@gmail.com> wrote:
> 
> Thank so much!
> This is exactly what I needed.
> What a gem :)
> 
> Best,
> Jen
> 
> On Tue, Jan 31, 2017 at 3:48 PM, Nikolaos Tur <nikolaos....@gmail.com 
> <mailto:nikolaos....@gmail.com>> wrote:
> Hi,
> 
> sorry for long delay answer. Solution which Peter suggested is absolutely 
> right - owner of packages has to add changes.
> Because I did not have any reaction to my message but needed quick solution 
> and wanted to stay in consistent with
> standard Galaxy installation procedure and neither do any fork of Daniel's 
> packages and setup then local toolsched 
> repository for tools or install these packages locally, I did some trick.
> 
> First I installed these packages. Installation of course failed. Then I open 
> them in web interface, uninstalled them, 
> modified  tool_dependencies.xml files (see below) and installed them again 
> from the web interface.
> Sorry if I miss something that was several months ago.
> 
> shell_command was modified.
> 
> ...
> <actions>
> <action type="shell_command">hg clone -r 
> ba0341816b15fff5e0a554658d6579a60e1b12b1 https://bitbucket.org/dan/pybamtools 
> <https://bitbucket.org/dan/pybamtools> pyBamTools</action>
> <action type="make_directory">$INSTALL_DIR/lib/python</action>
> <action type="shell_command">export 
> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && sed -i '/use_setuptools()/ 
> s/^/#/' setup.py && sed -i '/from distribute_setup import use_set
> uptools/ s/^/#/' setup.py && python setup.py install --home 
> $INSTALL_DIR</action>
> <action type="set_environment">
>     <environment_variable name="PYTHONPATH" 
> action="prepend_to">$INSTALL_DIR/lib/python</environment_variable>
> </action>
> </actions>
> ...
> 
> instead of 
> 
> <action type="shell_command">export 
> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install 
> --home $INSTALL_DIR</action>
> 
> Idea I think is clear, after clone of tools, modify first setup.py files and 
> then compile and install.
> 
> Hope it can be useful,
> Nikolaos.
> 
> On Tue, Jan 10, 2017 at 12:54 PM, Jennifer Hsieh <humbleambit...@gmail.com 
> <mailto:humbleambit...@gmail.com>> wrote:
> 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 
> <mailto: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/pybamtools/pull-requests/1/>
> -- https://bitbucket.org/dan/pybamparser/pull-requests/3/ 
> <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 
> <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 <tel:%2B27%2021%20447%203157>
> Cell: +27 74 841 4761 <tel:%2B27%2074%20841%204761>
> 
> 
> 
> 
> 
> ___________________________________________________________
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> 
> 
> -- 
> Peter Briggs peter.bri...@manchester.ac.uk 
> <mailto:peter.bri...@manchester.ac.uk>
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> 
> 
> 
> 
> -- 
> 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
> 
> 
> 
> ___________________________________________________________
> 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/
> 
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