On Apr 5, 2012, at 8:45 AM, Daniel Blankenberg wrote:
If you are designing a new datatype for a (set of) tool(s) and this datatype
requires a bunch of files to be in a directory and these files are generally
only useful when they are bundled together as a single unit (i.e. you
wouldn't
On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote:
I think I would approach the directory problem with a wrapper script that
takes arguments for each of the components needed by the tool.
The script could lay out the various files as expected in the working
directory and call the script. I
On Apr 4, 2012, at 11:03 AM, Langhorst, Brad wrote:
Maybe more a more specific example including all the files in the directory,
the input data, and the specific tool that will do the analysis would make
this clearer.
One particular tool is running pplacer
Hi Aaron,
If you are designing a new datatype for a (set of) tool(s) and this datatype
requires a bunch of files to be in a directory and these files are generally
only useful when they are bundled together as a single unit (i.e. you wouldn't
normally want any one of the files to exist as a
Hi,
I've been working off of a local instance of Galaxy (6799:40f1816d6857) to
develop tools and I'm running into some issues which I'm not sure how to
resolve idiomatically.
First, some of the tools I'm trying to write Galaxy wrappers for take a
directory as input. The directory contains
On Apr 4, 2012, at 11:11 AM, Langhorst, Brad wrote:
I'm no authority... but given that nobody else has replied yet I'll give my
opinion.
I think I would approach the directory problem with a wrapper script that
takes arguments for each of the components needed by the tool.
The script
On Apr 4, 2012, at 1:48 PM, Aaron Gallagher wrote:
On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote:
I think I would approach the directory problem with a wrapper script that
takes arguments for each of the components needed by the tool.
The script could lay out the various files as
On Apr 4, 2012, at 2:44 PM, Aaron Gallagher wrote:
On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote:
This is somewhat akin to the reference area galaxy uses to store reference
sequences (and their various indices, formats, annotations etc).
It might be possible to modify galaxy's
