1:38 p.m.
Hello,
Are there any existing Galaxy wrappers for the command line
tools (or the online services) TMHMM v2.0 (Trans-Membrane
Hidden Markov Model) and SignalP v3.0 (Signal Peptide)?
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
Both take protein FASTA files for input, but there are a few
extra considerations here like limiting each call to TMHMM
to 4000 proteins (IIRC), the possibility to split the job in order
to take advantage of multiple cores, and parsing the output
into a Galaxy friendly tabular form.
Thanks,
Peter
7:13 p.m.
Hello again Peter,
More great suggestions that we will consider for later enhancements.
Thanks for the feedback!
Best,
Jen
Galaxy team
On 9/9/10 6:38 AM, Peter wrote:
Hello,
Are there any existing Galaxy wrappers for the command line
tools (or the online services) TMHMM v2.0 (Trans-Membrane
Hidden Markov Model) and SignalP v3.0 (Signal Peptide)?
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
Both take protein FASTA files for input, but there are a few
extra considerations here like limiting each call to TMHMM
to 4000 proteins (IIRC), the possibility to split the job in order
to take advantage of multiple cores, and parsing the output
into a Galaxy friendly tabular form.
Thanks,
Peter
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Jennifer Jackson
http://usegalaxy.org
9:43 p.m.
On Fri, Oct 1, 2010 at 8:13 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote:
Hello again Peter,
More great suggestions that we will consider for later enhancements.
Thanks for the feedback!
Best,
Jen
Galaxy team
Hi Jen,
I was hoping for someone to say "yes, we did that for our Galaxy,
here is the wrapper code", but I'll settle for encouragement. ;)
As you will have seen, I'm focusing on the NCBI BLAST+
wrappers at the moment, but wrapping the command line
versions of TMHMM v2.0 and SignalP v3.0 would probably
be next on my list of things to do in Galaxy.
Peter
12:56 p.m.
On Fri, Oct 1, 2010 at 10:43 PM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
Hi Jen,
I was hoping for someone to say "yes, we did that for our Galaxy,
here is the wrapper code", but I'll settle for encouragement. ;)
As you will have seen, I'm focusing on the NCBI BLAST+
wrappers at the moment, but wrapping the command line
versions of TMHMM v2.0 and SignalP v3.0 would probably
be next on my list of things to do in Galaxy.
Peter
Hi all,
The TMHMM v2.0 and SignalP v3.0 tools are free to
download and use for academics, but commercial or
other users would need to negiotiate a license:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
There is nothing to stop me writing and sharing wrappers
for the tools, and installing and using TMHMM v2.0 and
SignalP v3.0 on a local Galaxy server for academic use.
However, I guess their licence would prevent TMHMM
v2.0 and SignalP v3.0 being included in the "public"
Galaxy server? One option might be to ask CBS if
they would allow Penn State University to make these
tools available via their public Galaxy server.
Has this issue of "academic only" licences come up
before for Galaxy wrapped tools?
Alternatively I might be able to write wrappers for the
CBS hosted TMHMM and SignalP webservice which
appears to be free to use by anyone, but that seems
less robust and they may be unhappy with the likely
increased usage.
Peter
8:12 p.m.
Hi Peter,
Good question about licenses! Sorry for the delayed answer, we had a bit
of discussion to review the existing strategy.
The general guiding policy is that if a tool is not completely public,
then it will not be released to the main code base/servers.
That said, you are correct - if something can be worked out with tool
author, coordination for a fully integrated wrapper is possible. Same
would be true for remote use of a 3rd party web tool - coordination with
the authors/owner would be needed first (although this is not the ideal
solution for galaxy main).
Meanwhile, a great place to add wrappers/remote access tools that have
special licensing is the tool shed (http://community.g2.bx.psu.edu/).
The user comments field (displayed as Description) is free-form text and
any credits/license pointers can be added there for now. We may add in a
special field for this info later on, but for immediate use this is a
visible key that will likely satisfy many licensing rules.
Thanks again for more great ideas!
Jen
Galaxy team
On 10/14/10 5:56 AM, Peter wrote:
On Fri, Oct 1, 2010 at 10:43 PM,
Peter<peter(a)maubp.freeserve.co.uk> wrote:
>
> Hi Jen,
>
> I was hoping for someone to say "yes, we did that for our Galaxy,
> here is the wrapper code", but I'll settle for encouragement. ;)
>
> As you will have seen, I'm focusing on the NCBI BLAST+
> wrappers at the moment, but wrapping the command line
> versions of TMHMM v2.0 and SignalP v3.0 would probably
> be next on my list of things to do in Galaxy.
>
> Peter
>
Hi all,
The TMHMM v2.0 and SignalP v3.0 tools are free to
download and use for academics, but commercial or
other users would need to negiotiate a license:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
There is nothing to stop me writing and sharing wrappers
for the tools, and installing and using TMHMM v2.0 and
SignalP v3.0 on a local Galaxy server for academic use.
However, I guess their licence would prevent TMHMM
v2.0 and SignalP v3.0 being included in the "public"
Galaxy server? One option might be to ask CBS if
they would allow Penn State University to make these
tools available via their public Galaxy server.
Has this issue of "academic only" licences come up
before for Galaxy wrapped tools?
Alternatively I might be able to write wrappers for the
CBS hosted TMHMM and SignalP webservice which
appears to be free to use by anyone, but that seems
less robust and they may be unhappy with the likely
increased usage.
Peter
--
Jennifer Jackson
http://usegalaxy.org
8:46 a.m.
On Fri, Oct 22, 2010 at 9:12 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote:
Hi Peter,
Good question about licenses! Sorry for the delayed answer, we had a bit of
discussion to review the existing strategy.
The general guiding policy is that if a tool is not completely public, then
it will not be released to the main code base/servers.
As I expected - thanks for the clarification.
That said, you are correct - if something can be worked out with
tool
author, coordination for a fully integrated wrapper is possible. Same would
be true for remote use of a 3rd party web tool - coordination with the
authors/owner would be needed first (although this is not the ideal solution
for galaxy main).
OK
Meanwhile, a great place to add wrappers/remote access tools that
have
special licensing is the tool shed (http://community.g2.bx.psu.edu/). The
user comments field (displayed as Description) is free-form text and any
credits/license pointers can be added there for now. We may add in a special
field for this info later on, but for immediate use this is a visible key
that will likely satisfy many licensing rules.
Good idea. Can you (or someone at Galaxy) add another category?
Something like "Sequence analysis", or "Protein sequence analysis"
seems appropriate to me.
Thanks,
Peter
9:49 a.m.
On Mon, Oct 25, 2010 at 9:46 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
> Meanwhile, a great place to add wrappers/remote access tools that have
> special licensing is the tool shed (http://community.g2.bx.psu.edu/).
Good idea. Can you (or someone at Galaxy) add another category?
Something like "Sequence analysis", or "Protein sequence analysis"
seems appropriate to me.
Thank you to Jennifer for adding that section.
I submitted a "tool suite" containing my TMHMM 2.0 and SignalP 3.0
wrappers last week - currently in status "waiting" so not publicly
visible yet.
Peter
11:11 a.m.
On Mon, Nov 8, 2010 at 9:49 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
Thank you to Jennifer for adding that section.
I submitted a "tool suite" containing my TMHMM 2.0 and SignalP 3.0
wrappers last week - currently in status "waiting" so not publicly
visible yet.
And it is now online at http://community.g2.bx.psu.edu/
Thanks to whomever from Galaxy did the review, I guess there were
no comments which I hope is a good sign.
Peter
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