Re: [galaxy-dev] STACKS error
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 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" > *À: *"Yvan Le Bras" > *Cc: *"Amogelang Raphenya" , > 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 > 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" > > 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 > > from stacks import * > > File > > "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py > ", > > line 19, in > > 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 inte
Re: [galaxy-dev] STACKS error
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 +
+++ 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"
*À: *"Yvan Le Bras"
*Cc: *"Amogelang Raphenya" ,
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
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"
> 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
> from stacks import *
> File
>
"/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py",
> line 19, in
> 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
Re: [galaxy-dev] STACKS error
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" > À: "Yvan Le Bras" > Cc: "Amogelang Raphenya" , > 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 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" > > 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 > > from stacks import * > > File > > "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py", > > line 19, in > > 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 ___ 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/
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 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" > 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 > from stacks import * > File > "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py", > line 19, in > 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/ ___ 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/
Re: [galaxy-dev] STACKS error
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 - Mail original - > De: "Amogelang Raphenya" > 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 > from stacks import * > File "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py > ", line 19, in > 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/
[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 from stacks import * File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py", line 19, in 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/
