Ummm... I think it is that the VM started shipping with an
incompatible paramkio. Saket I think you were using -m like it were
-c?

> python -m "import string" # what you had
/usr/bin/python: No module named import string
> python -c "import string
> python -m "string"
>

Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
and it works fine (reran today
https://travis-ci.org/jmchilton/bwa-mem/builds/37353814) - so I
suggest creating a virtualenv and testing Galaxy inside of that.

Hope this helps.

-John


On Mon, Nov 17, 2014 at 12:52 PM, Saket Choudhary <sake...@gmail.com> wrote:
> I have had the same issue. A little debugging here:
> https://travis-ci.org/saketkc/galaxy_tools/builds/41209515#L84
>
> I first thought that there was a conflict with system installed
> paramiko, but it is not:
> https://travis-ci.org/saketkc/galaxy_tools/builds/41210153#L60
>
> A clean install of galaxy-central worked fine on Mac, I am yet to test
> this on a local linux installation though.
>
>
> On 17 November 2014 03:57, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hello all,
>>
>> There looks to be an egg problem with the latest galaxy-central,
>> here are excepts from a failed Galaxy install on my TravisCI test
>> setup,
>> https://travis-ci.org/peterjc/pico_galaxy/builds/41233860
>>
>> Here's another project build with the same error:
>> https://travis-ci.org/peterjc/galaxy_blast/builds/41235899
>>
>> $ ./run.sh --stop-daemon || true
>> Initializing config/migrated_tools_conf.xml from 
>> migrated_tools_conf.xml.sample
>> ...
>> Initializing static/welcome.html from welcome.html.sample
>> Some eggs are out of date, attempting to fetch...
>> Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg
>> Fetched 
>> http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
>> Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
>> Fetched 
>> http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
>> Traceback (most recent call last):
>>   File "./scripts/fetch_eggs.py", line 46, in <module>
>>     c.resolve() # Only fetch eggs required by the config
>>   File 
>> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 347, in resolve
>>     egg.resolve()
>>   File 
>> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 192, in resolve
>>     if e.args[1].key != e.args[0].key:
>> IndexError: tuple index out of range
>> Fetch failed.
>> No PID file exists in paster.pid
>>
>>
>> $ python scripts/fetch_eggs.py
>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
>> Traceback (most recent call last):
>>   File "scripts/fetch_eggs.py", line 46, in <module>
>>     c.resolve() # Only fetch eggs required by the config
>>   File 
>> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 347, in resolve
>>     egg.resolve()
>>   File 
>> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 192, in resolve
>>     if e.args[1].key != e.args[0].key:
>> IndexError: tuple index out of range
>>
>> The command "python scripts/fetch_eggs.py" failed and exited with 1
>>
>> Looking at http://eggs.galaxyproject.org/MarkupSafe/ for
>> Python 2.7 and Linux x86_64 there is a ucs4 egg:
>>
>> MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg        09-Jun-2011 03:09
>>             30724
>>
>> So, why is this failing? Not I am not explicitly installing MakupSafe
>> (so I do not expect there to be a conflicting version installed).
>>
>> Also it would seem there is a bug in the resolve method assuming that
>> e.arg will always have (at least) two entries?
>>
>> Thanks,
>>
>> Peter
>> ___________________________________________________________
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
  http://lists.bx.psu.edu/

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

Reply via email to