Do you have virtualenv installed and available to planemo? If not,
might be worth reviewing this thread -
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?
On Fri, Nov 20, 2015 at 2:27 PM, Christian Brenninkmeijer
I have gotten past this stage and an now getting errors which may be
The fix was to edit
There may well be other missing as well so that needs a look.
For example in the old version I found an egg
From: Peter Cock [p.j.a.cock(a)googlemail.com]
Sent: Friday, November 20, 2015 12:41 PM
To: Christian Brenninkmeijer
Cc: John Chilton; galaxy-dev(a)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:
Perhaps a more recent version of nose is needed?
On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
> Hi Peter/ John
> requirementx.txt already includes the latest version of nose
> It is nose that is complaining it does not like the sys,args passed in by
> From: Peter Cock [p.j.a.cock(a)googlemail.com]
> Sent: Friday, November 20, 2015 11:30 AM
> To: Christian Brenninkmeijer; John Chilton
> Cc: galaxy-dev(a)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(a)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
>> 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:
> @John: My guess is we need to add "nose" to planemo's requirements.txt
> to ensure this gets installed automatically?