Re: [galaxy-dev] Contribution of tools to galaxy main server
Hello Dongjun, Thanks very much for your interest in sharing this tool with the Galaxy community. At this time the process for sharing tools is to upload your tool to the Galaxy tool shed at http://toolshed.g2.bx.psu.edu/. Ideally your tool will include functional tests and your tool shed repository will include small input / output datasets for these tests. If your tool uses any 3rd party dependencies, the <requirements> tag set in the tool config should reflect them appropriately. For clarification on tool config syntax, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax. In the past, the process used by the core Galaxy development team to share tools was to include them in the Galaxy distribution, but we are beginning to phase this process out, replacing it with the tool shed. Over time we will be eliminating tools from the distribution, and local Galaxy instances will install them from the Galaxy tool shed. This same process will be used for populating our main Galaxy instance here at Penn State with tools. So for now, please upload your tool to the tool shed. Thanks again, Greg Von Kuster On Sep 9, 2011, at 4:08 PM, Dongjun Chung wrote:
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.1002...
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.
See http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement...
Thanks!
Best, Dongjun ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Thank you for the clarification. Our tool contains appropriate function tests & utilizes <requirements> tags and it is just contributed to galaxy tool shed. Thank you again for your help. Dongjun Chung On 09/14/2011 08:18 AM, Greg Von Kuster wrote:
Hello Dongjun,
Thanks very much for your interest in sharing this tool with the Galaxy community. At this time the process for sharing tools is to upload your tool to the Galaxy tool shed at http://toolshed.g2.bx.psu.edu/. Ideally your tool will include functional tests and your tool shed repository will include small input / output datasets for these tests. If your tool uses any 3rd party dependencies, the <requirements> tag set in the tool config should reflect them appropriately. For clarification on tool config syntax, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax.
In the past, the process used by the core Galaxy development team to share tools was to include them in the Galaxy distribution, but we are beginning to phase this process out, replacing it with the tool shed. Over time we will be eliminating tools from the distribution, and local Galaxy instances will install them from the Galaxy tool shed. This same process will be used for populating our main Galaxy instance here at Penn State with tools. So for now, please upload your tool to the tool shed.
Thanks again,
Greg Von Kuster
On Sep 9, 2011, at 4:08 PM, Dongjun Chung wrote:
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.1002...
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 <mailto: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 <mailto:dongjun.chung@gmail.com>> Cc: galaxy-dev@lists.bx.psu.edu <mailto: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.
See http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement...
Thanks!
Best, Dongjun ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu <mailto:greg@bx.psu.edu>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu <mailto:greg@bx.psu.edu>
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Greg Von Kuster