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 <saketkc@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.cock@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 Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch...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-li... 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.... 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/

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On Mon, Nov 17, 2014 at 7:23 PM, John Chilton <jmchilton@gmail.com> wrote:

Ummm... I think it is that the VM started shipping with an incompatible paramkio.

[...]

Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv and it works fine [...]

That's a useful workaround, but a virtualenv is not viable for existing Galaxy installations - which may also come to have this problem if their system copy of paramiko is updated? I'm not familiar with paramiko or markupsafe, but if there is a conflict it would be good to have a direct fix. Peter