Hi Yvan,

We had this issue as well, and fixed it for now by adding the checkers.py from an old galaxy server. I've added it in attachment if you don't have it anymore.

put it in "galaxy-dist/lib/galaxy/datatypes/checkers.py"

If relevant, I also made a few changes to the stacks script itself, but I can't remember if is was related (I think due to ordereddict module in different python versions)

diff -r 0e0ff9e9c761 stacks.py --- a/stacks.py Mon Sep 28 13:21:35 2015 +0000 +++ b/stacks.py Fri May 20 17:53:56 2016 +0200 @@ -14,6 +14,8 @@ import os, sys, re, shutil import glob import collections +import ordereddict +from ordereddict import OrderedDict import gzip, zipfile, tarfile import subprocess from galaxy.datatypes.checkers import * @@ -31,7 +33,8 @@ """ def galaxy_config_to_tabfiles(input_config):

- tab_files=collections.OrderedDict() + #tab_files=collections.OrderedDict() + tab_files=OrderedDict() for line in open(input_config, "r").readlines(): if line.strip() != '': extract=line.strip().split("::") @@ -43,7 +46,8 @@

def galaxy_config_to_tabfiles_for_STACKS(input_config):

- tab_files=collections.OrderedDict() + #tab_files=collections.OrderedDict() + tab_files=OrderedDict() for line in open(input_config, "r").readlines(): if line.strip() != '': extract=line.strip().split("::")

On 2016-05-20 17:28, Yvan Le Bras 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) . 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, 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:
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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

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