Sorry for bothering you, but I have encountered some difficulties in using STACKS at galaxy (local instance). I am new to STACKS and Galaxy (and totally ignorant to programming), this problem has been troubling me for a few days. and wish anyone could advice to fix it.
I installed STACKS from GUGGO tool shed to Galaxy, I think it is Stacks 1.18 version, but I was not able to install Package_bwa_0_6_2 into galaxy. Is STACKs bonded with version 0_6_2? This is not a big issue as I could use other aligners to map the RAD reads to a reference genome, and import the SAM files to data library.
When I deploy STACKS : Reference map, I was returned an error massage:
error
An error occurred with this dataset:
Users/218496f/shed_tools/toolshed.genouest.org/repos/cmonjeau/stacks/4bbc09fa9b80/stacks/STACKS_refmap.py", line 16, in <module> from galaxy.datatypes.checkers import *
ImportError: no module named checkers.
I then managed to get a file called “checkers.py” into galaxy/lib/galaxy/datatypes
But that did not help, I still could not get it work, with an error message:
error
An error occurred with this dataset:
Users/218496f/shed_tools/toolshed.genouest.org/repos/cmonjeau/stacks/4bbc09fa9b80/stacks/STACKS_refmap.py", line 16, in <module> from galaxy.datatypes.checkers import *
File "/Users/218496f/galaxy/lib/gal
I wish someone could advise on how to fix it.
Thank you
Tianhua
This seems like a missing dependency ... best is to contact the guys behind this ToolShed.