i gave it a bad name previously and peter didn't find it in a search at first, but i couldn't change the name, so i created a new repository.  i put a note in the old repo (hmmscan), referring to the new repo (hmmer).  that may suffice. however you folks how you want to handle it is fine.

On Tue, Mar 6, 2012 at 3:38 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:

Hi Ed,

Do you want the hmmscan repository itself deleted?  It's been downloaded / cloned 86 times, although it is never been automatically installed into a local Galaxy since the contained tool does not properly load into Galaxy.  We generally do not like to delete things like this because doing do prevents reproducibility.  I'm looking for feedback from the community on this one - does eliminating this repository affect anyone?

Thanks for the new contributions tot he tool shed!

Greg Von Kuster

On Mar 6, 2012, at 1:47 AM, Edward Kirton wrote:

i created a new toolshed repo, hmmer since i couldn't rename it.  as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress.  will add hmmbuild, hmmalign asap; others upon request.

dave, is there a way to delete an old tool?  (hmmscan) 

On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskirton@lbl.gov> wrote:

great suggestion; i'll make those changes

On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
> hi, peter - i will fix the description and upload hmmsearch and infernal
> today.

Great.

Assuming hmmscan and hmmsearch have (almost) the same command
line API, there is something to be said for presenting them as one tool
in Galaxy, with a drop down selection between them (with help text
about which is recommend adapted from the HMMER blog post). One
could even have an automatic selection by a wrapper script based on
the number of query sequences and the number of HMMs. My thinking
here is the detail of hmmscan vs hmmsearch is purely an implementation
detail that the end user shouldn't have to worry about.

Or just duplicate most of the XML code and have two wrappers. But
as far as I know there isn't (yet) a nice way of reusing XML snippets
between tool wrappers... which would be handy.

Thanks,

Peter

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