On Tuesday, June 28, 2016, Olivier Sallou <olivier.sal...@irisa.fr> wrote:
> > > ------------------------------ > > *De: *"Michael Crusoe" <michael.cru...@gmail.com > <javascript:_e(%7B%7D,'cvml','michael.cru...@gmail.com');>> > *À: *"Olivier Sallou" <olivier.sal...@irisa.fr > <javascript:_e(%7B%7D,'cvml','olivier.sal...@irisa.fr');>> > *Cc: *"Debian Med Project List" <debian-med@lists.debian.org > <javascript:_e(%7B%7D,'cvml','debian-med@lists.debian.org');>>, "Nate > Coraor" <n...@bx.psu.edu <javascript:_e(%7B%7D,'cvml','n...@bx.psu.edu');> > > > *Envoyé: *Lundi 27 Juin 2016 21:04:21 > *Objet: *Re: Galaxy project producing their own Debian packages > > Python packages that need packaging: > > bx-python > wchartype > dictobj > bioblend > requests-toolbelt > pulsar-galaxy-lib > sqlalchemy-migrate > svgwrite > > > you mean all other Galaxy dependencies are already available as packages > and only those ones are missing in Debian ? > Correct > an other point is Galaxy uses specific versions of packages (which is > quite usual), but may not work with latest releases of those. Would need > testing. > Thankfully in the last few months we have updated to using recent versions of our dependencies. The goal is to be compatible with current versions of our dependencies going forward. > We would need in Debian to deactivate Galaxy startup in virtualenv as well > as skip any auto install. > The auto-install of dependencies and creation of a virtualenv only happens when running from source. If installed as a traditional Python package, it should behave normally. --nate > Olivier > > > This should a complete list, Nate promises that there are no hidden sub > dependencies. > > They also use a custom fork of pysam > > On Mon, Jun 27, 2016 at 2:34 PM, Michael Crusoe <michael.cru...@gmail.com > <javascript:_e(%7B%7D,'cvml','michael.cru...@gmail.com');>> wrote: > >> Hoopla, >> >> I'm at the Galaxy Community Conference sitting next to Nate Coraor. >> >> Nate is enthusiastic about Galaxy becoming properly packaged for Debian. >> He is well aware of how hacky his current package is :-) >> >> On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou <olivier.sal...@irisa.fr >> <javascript:_e(%7B%7D,'cvml','olivier.sal...@irisa.fr');>> wrote: >> >>> >>> >>> On 06/16/2016 08:43 AM, Michael Crusoe wrote: >>> > >>> > Vezi Tweetul lui @natefoo: >>> > https://twitter.com/natefoo/status/743306923026440194 >>> > >>> > https://depot.galaxyproject.org/nate/dpkg/ >>> > >>> nice, but easy for them. Galaxy installs many things at run time from >>> remote locations (pypi and others). So not easy to fit in Debian as all >>> dependencies not to be Debian packages. >>> >>> Olivier >>> >>> -- >>> Olivier Sallou >>> IRISA / University of Rennes 1 >>> Campus de Beaulieu, 35000 RENNES - FRANCE >>> Tel: 02.99.84.71.95 >>> >>> gpg key id: 4096R/326D8438 (keyring.debian.org) >>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 >>> >>> >> >> >> -- >> Michael R. Crusoe >> Community Engineer & Co-founder >> Common Workflow Language project >> https://impactstory.org/u/0000-0002-2961-9670 >> michael.cru...@gmail.com >> <javascript:_e(%7B%7D,'cvml','michael.cru...@gmail.com');> >> +32 (0) 2 808 25 58 >> +1 480 627 9108 >> > > > > -- > Michael R. Crusoe > Community Engineer & Co-founder > Common Workflow Language project > https://impactstory.org/u/0000-0002-2961-9670 > michael.cru...@gmail.com > <javascript:_e(%7B%7D,'cvml','michael.cru...@gmail.com');> > +32 (0) 2 808 25 58 > +1 480 627 9108 > > >
