Dear Greg von Kuster,
Hello, this is Dongjun Chung, a PhD student at the
University of Wisconsin-Madison.
We recently developed a tool for galaxy and hope to
contribute our tool to galaxy main server. We have
developed a tool for allocation of multi-reads (reads that
map to multiple locations on the reference genome) in
ChIP-seq. In contrast, basically all the currently
available ChIP-seq peak callers utilize only uni-reads
(reads the map to a unique location on the reference
genome). This tool implements our paper recently published
in PLoS computational biology:
Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E,
Dewey C, and Keles S (2011), “Discovering transcription
factor binding sites in highly repetitive regions of
genomes with multi-read analysis of ChIP-Seq data,” PLoS
Computational Biology, 7(7): e1002111.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002111
We believe that our tool could be appropriate for galaxy
main server because there is no tool for this purpose in
the server yet and this tool should be beneficial to
general galaxy users, especially researchers studying
eukaryotic genomes. We already completed developing
corresponding wrapper and tool definition files for
galaxy. Our tool can accept FASTA/FASTQ as input and its
output can also work nicely with diverse ChIP-seq peak
callers such as MACS peak caller which is already in the
galaxy main server.
If the galaxy development team can accept our tool as a
part of galaxy in the main server, please let us know
anything you need for us to contribute our tool to galaxy.
We can prepare what is needed to meet the requirements.
Sincerely,
Dongjun Chung
PhD student
Department of Statistics
University of Wisconsin-Madison
On 09/09/2011 12:59 PM, Dongjun Chung wrote:
---------- Forwarded message
----------
From:
Greg Von Kuster
<greg@bx.psu.edu>
Date: Wed, Aug 31, 2011 at 2:38 PM
Subject: Re: [galaxy-dev] contribute tools to galaxy?
To: Dongjun Chung <
dongjun.chung@gmail.com>
Cc:
galaxy-dev@lists.bx.psu.edu
Hello Dongjun, see
my answers to your question inline.
On Aug 28, 2011, at 10:12 AM, Dongjun
Chung wrote:
Hi All,
I'm a newbie to galaxy and enjoying it a lot
these days. Thanks for the great work.
I have a question regarding contribution of
software to galaxy. We developed a ChIP-seq
peak calling algorithm and software (R
package) and hope to contribute it to
galaxy. I have read the wiki and prior
mailing list about the contribution system
but it is still somewhat confusing to me.
1. It seems that I can contribute our
software to "tool shed" if I prepare
appropriate code & definition files.
Then, users can download and use it with
their locally installed galaxy. However,
these files committed to tool shed will not
appear in galaxy main or test servers. Am I
correct?
Tools from the Galaxy tool shed may or may not
be available in the Galaxy test / main servers
hosted at Penn State.
2. What is clear relationship between
main/test servers & tool shed?
The Galaxy tool shed enables the Galaxy
community to share tools. These tools are
generally used in local Galaxy installations,
but not available on the Penn State instances.
Can we contribute our
software to main or test servers as well?
The tools available on the Penn State
servers are generally developed by the Galaxy
core development team, and are available in
the Galaxy distribution. If your tools
complement the tools currently available in
the distribution, the Galaxy core development
team may agree to include them. However, see
my comments 2 answers below regarding upcoming
enhancements to Galaxy and the tool shed.
Or only galaxy core
developers can add new tools to galaxy main
or test servers?
Yes.
If so, which software
is considered to be added to servers? Are
they chosen from tools contributed to tool
shed?
Currently, tools available in the distribution
and on the Penn State instances are generally
developed by the core Galaxy development team.
However, upcoming enhancements to Galaxy and
the Galaxy tool shed will enable automatic
installation of tools from the tool shed into
local Galaxy instances, eliminating the
necessity to include tools in the distribution.
This automation will be available fairly soon.
3. If our software is a R package, then
users need to download and install it first
in their R system before they use our
software within their galaxy system even in
the case they have appropriate definition
files. Am I right? Or is there any better
solution for this?
If your tools require R, then those that use
your tools will need to install R in the Galaxy
environment path so the tools will be
functional. Tools that have dependencies like
this should include a <requirements> tag
set in the tool config.
Thanks!
Best,
Dongjun
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