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_bras@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" 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@irisa.fr
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@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