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 ) . I cc Ralf concerning this. Cheers, Yvan ----- Mail original -----
De: "John Chilton" <jmchilton@gmail.com> À: "Yvan Le Bras" <yvan.le_bras@irisa.fr> Cc: "Amogelang Raphenya" <raphenar@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_bras@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" <raphenar@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: raphenar@mcmaster.ca skype: amos_raphenya
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-- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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_bras@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/
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-- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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_bras@irisa.fr