Do you have virtualenv installed and available to planemo? If not, might be worth reviewing this thread - http://dev.list.galaxyproject.org/Planemo-0-20-0-and-xunit-td4668334.html and installing it. In dev, virtualenv is a hard dependency for running Galaxy and this is new, in the past Galaxy would run without it. We (Nate) may find a way around this before the next release (16.01) specifically to allow Galaxy to run in anaconda based environments. If you have virtualenv installed, I really don't think Galaxy's dependency list should require modification especially for Python 2.7, is this for Linux or Mac OS X? -John On Fri, Nov 20, 2015 at 2:27 PM, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk> wrote:
I have gotten past this stage and an now getting errors which may be my own.
The fix was to edit https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/req... and add twill==1.8.0 lxml==3.5.0 cssselect==0.9.1 NoseHTML==0.4.2
There may well be other missing as well so that needs a look. For example in the old version I found an egg NoseTestDiff-0.1-py2.7.egg
Christian ________________________________________ From: Peter Cock [p.j.a.cock@googlemail.com] Sent: Friday, November 20, 2015 12:41 PM To: Christian Brenninkmeijer Cc: John Chilton; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
Which file are you looking at? There is no nose entry here:
https://github.com/galaxyproject/planemo/blob/master/requirements.txt
Perhaps a more recent version of nose is needed?
Peter
On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk> wrote:
Hi Peter/ John requirementx.txt already includes the latest version of nose
nose==1.3.7
It is nose that is complaining it does not like the sys,args passed in by FunctionalTest.py
Christian
________________________________________ From: Peter Cock [p.j.a.cock@googlemail.com] Sent: Friday, November 20, 2015 11:30 AM To: Christian Brenninkmeijer; John Chilton Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk> wrote:
Hi All,
I am unable to run Planemo against the latest dev branch.
1. import twill error
I was able to fix this by adding to requirements.txt twill==1.8.0 lxml==3.5.0 cssselect==0.9.1
But then I get
functional_tests.py: error: no such option: --with-nosehtml functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests Traceback (most recent call last): ... SystemExit: 2
That's not a very helpful error, is it? It reminds me of a missing dependency / installation problem I had long ago when first setting up TravisCI to run Galaxy tool tests:
https://github.com/peterjc/pico_galaxy/commit/c8265f4a42caf62eb3bc8b36b475f1...
@John: My guess is we need to add "nose" to planemo's requirements.txt to ensure this gets installed automatically?
Peter