Oops forgot to cc the list. On Nov 18, 2014 7:26 AM, "John Chilton" <jmchilton@gmail.com> wrote:
I will admit to not actually understanding Galaxy's dependency management but I think virtualenv is exactly the advice people who do understand it give http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html. It is a widely used tool precisely designed to solve such problems - I think it is the best way to go. I don't know why it would not be appropriate for existing installations - I think it is in fact somethimg of a "best practice" for existing installations.
Certainly that error message should be more helpful but I am not sure we should do anything to address this beyond that - do you have a particular idea in mind? On Nov 18, 2014 5:49 AM, "Peter Cock" <p.j.a.cock@googlemail.com> wrote:
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