Hi Yvan, Thanks for including me in this conversation. I'll keep an eye on this and will make the necessary changes in our next commit/version.
Best wishes, Ralf On 20 May 2016 at 23:28, Yvan Le Bras <yvan.le_b...@irisa.fr> wrote: > Thank you John for the rapid answer and the PR! > > I have had the same issue trying installing and use a Galaxy-M instance ( > <https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0115-8> > https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0115-8) > . I cc Ralf concerning this. > > Cheers, > > Yvan > > ------------------------------ > > *De: *"John Chilton" <jmchil...@gmail.com> > *À: *"Yvan Le Bras" <yvan.le_b...@irisa.fr> > *Cc: *"Amogelang Raphenya" <raphe...@mcmaster.ca>, > galaxy-dev@lists.galaxyproject.org > *Envoyé: *Vendredi 20 Mai 2016 17:15:19 > *Objet: *Re: [galaxy-dev] STACKS error > > This is one the reasons (though not the only one) I generally > discourage putting datatypes in the tool shed - Galaxy isn't very > clear about what interface it provides to datatypes and it would seem > very difficult from my perspective to maintain that interface and grow > Galaxy at the same time. > > This checkers module though is clearly useful to datatypes and it is > quite trivial to provide backward compatibility so I've opened a PR to > the new 16.04 release to restore this module - > https://github.com/galaxyproject/galaxy/pull/2389. > > Sorry for the inconvenience. > > -John > > > On Fri, May 20, 2016 at 10:45 AM, Yvan Le Bras <yvan.le_b...@irisa.fr> > wrote: > > Hi Amos, > > > > Thanks to use Stacks on Galaxy! I already seen this error. This is due, I > > think, to newest Galaxy versions who don't have the checkers.py anymore > on > > the datatypes folder.... Thios can be fixed using an older Galaxy > version... > > Otherwise, we are working on a new version of the Stacks Galaxy tools... > who > > will be usable in the upcoming days.... or not ;) > > > > Cheers, > > > > Yvan > > > > > > ________________________________ > > > > De: "Amogelang Raphenya" <raphe...@mcmaster.ca> > > À: galaxy-dev@lists.galaxyproject.org > > Envoyé: Vendredi 20 Mai 2016 16:37:04 > > Objet: [galaxy-dev] STACKS error > > > > > > Anyone encountered this error? > > > > Fatal error: Exit code 1 (Error in Stacks Process radtag execution) > > Traceback (most recent call last): > > File > > "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py > ", > > line 16, in <module> > > from stacks import * > > File > > "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py > ", > > line 19, in <module> > > from galaxy.datatypes.checkers import * > > ImportError: No module named checkers > > > > > > Cheers. > > > > > > Amos Raphenya, B.Eng > > Bioinformatics Software Developer > > Department of Biochemistry & Biomedical Sciences > > McMaster University, MDCL 2317 > > p: (905) 525-9140 > > a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1 > > e: raphe...@mcmaster.ca > > skype: amos_raphenya > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > > > > > > > -- > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Yvan Le Bras, PhD > > @Yvan2935 > > <°))))>< > > e-Biogenouest project > > http://www.e-biogenouest.org > > CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, > 35042 > > Rennes Cedex > > tél.: +33 (0) 2 99 84 71 79 / > +33 > > (0) 6.10.43.96.51 > > > > yvan.le_b...@irisa.fr > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > > -- > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > Yvan Le Bras, PhD > > @Yvan2935 > > <°))))>< > e-Biogenouest project > http://www.e-biogenouest.org > CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, > 35042 Rennes Cedex > tél.: +33 (0) 2 99 84 71 79 / +33 > (0) 6.10.43.96.51 > > yvan.le_b...@irisa.fr > >
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