Hello Dan

Thanks for merging in the changes, just to let you know that these packages 
seem to install okay for me now from the toolshed - much appreciated!

Best wishes

Peter

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

________________________________
From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Friday, February 03, 2017 2:46 PM
To: Jennifer Hsieh
Cc: Nikolaos Tur; Galaxy Dev List; Peter Briggs
Subject: Re: [galaxy-dev] Request more details from Nikolaos Tur about 
pyBamTools & pyBamParser dependency packages message

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<mailto: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 
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/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<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


___________________________________________________________
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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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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