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
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 sep
On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote:
> Given that it describes where the rest of the files are, maybe it would work
> to pass only the CONTENTS.json file.
> Then you can just build your references in a directory structure on a shared
> file system and keep absolute paths in the C
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 (https://github.com/matsen/pplac
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.
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
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
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 scri
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 could lay out the various files as expected in the working dire
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 some
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