Hi John, Yes i have vitrualenv installed. I tried planemo both using : brew tap galaxyproject/tap brew install planemo And using: virtualenv .venv; . .venv/bin/activate pip install planemo With the exact same results I also have not trouble running galaxy without the extra. bit in galaxy's requiremets.txt It is Planamo that fails. But only in the builds since this weekend. Early Galaxy builds work fine. Christian PS. Ubuntu and python 2.7 ________________________________________ From: John Chilton [jmchilton@gmail.com] Sent: Friday, November 20, 2015 2:53 PM To: Christian Brenninkmeijer Cc: Peter Cock; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev 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