Greg and Björn, thanks for the info. I will again review that section. Indeed a simple tool just required an xml, tool script and some README. But as you guessed I was more interested in complexer types; One might be the use of a bowtie2 multi mapper script we use to map fastq reads to a set of databases picked from the available bowtie indices within galaxy. Graphs are generated with R. So of course the xml and wrapper scripts should be there as well as the R scripts. How about bowtie2_db.lock additions? How to secure R and bowtie2? Just by requirements? And their licenses? Thanks Alex Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 4 februari 2013 16:25 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission Hello Alex, In very general terms, a repository should include everything necessary for ensuring each if it's contained utilities is functionally correct when installed into a local Galaxy instance. Categories of Galaxy utilities are Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 3rd-party tool dependency definitions and repository dependency definitions. I believe the content of the original tool shed wiki is mostly retained in the current wiki. The original wiki was just divided into document sections, and a lot of new content has been added because of the many new tool shed features that have been introduced. The main section detailing repository content it is here: http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_rep.... This page include many related pages whose links are at the bottom of the page. It is not possible to give a precise, but general definition of what should be included in all repositories because repositories can contain different types of Galaxy utilities. Each of the sections of the wiki page link above describes how to include these various Galaxy utilities. Even Galaxy tools fall into various categories. For example, some are very simple, requiring no 3rd party tool dependencies and the tool form does not use dynamically generated select lists. These generally only require a script and an XML file. However, more complex Galaxy tools may require additional supporting content to be included in the repository (e.g., a tool_data_table_conf.xml.sample file. etc) If you could provide more details about what types of utilities you are building, I can steer you to the wiki pages that provide information about those specific utilities. Thanks! Greg Von Kuster On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote: Hi All, We are experimenting with local toolsheds for tool maintainability. On the old galaxy wiki I can remember there was a short tutorial or small description of the minimal requirements of a tool to be submitted to the toolshed. Actually we submitted some. However we seem unable to retrieve the proper info from the updated wiki. We did find info on single tools or suites, or more special cases, but a simple example/list of how and what to include in a repository is missing (at least we cannot find it....might be an issue of wrong key words).. Anyone has an idea where to find such a document? Thanks Alex ___________________________________________________________ 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: http://lists.bx.psu.edu/

Hi Alex, On Feb 4, 2013, at 10:35 AM, Bossers, Alex wrote:

Greg and Björn, thanks for the info.

I will again review that section. Indeed a simple tool just required an xml, tool script and some README. But as you guessed I was more interested in complexer types; One might be the use of a bowtie2 multi mapper script we use to map fastq reads to a set of databases picked from the available bowtie indices within galaxy. Graphs are generated with R.

So of course the xml and wrapper scripts should be there as well as the R scripts.

R scripts are defined as tool dependencies that are contained within the same repository. See http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_incl...

How about bowtie2_db.lock additions?

This is defined as a 3rd-party tool dependency, and you can include a file named tool_dependencies.xml that defines how to install and compile it and ensure your appropriate repository tool can locate the compiled dependency. See http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too...

How to secure R and bowtie2? Just by requirements?

Can you clarify this question?

And their licenses?

See http://wiki.galaxyproject.org/ToolShedReadmeFiles

Thanks Alex

Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 4 februari 2013 16:25 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission

Hello Alex,

In very general terms, a repository should include everything necessary for ensuring each if it's contained utilities is functionally correct when installed into a local Galaxy instance. Categories of Galaxy utilities are Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the current wiki. The original wiki was just divided into document sections, and a lot of new content has been added because of the many new tool shed features that have been introduced. The main section detailing repository content it is here: http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_rep.... This page include many related pages whose links are at the bottom of the page.

It is not possible to give a precise, but general definition of what should be included in all repositories because repositories can contain different types of Galaxy utilities. Each of the sections of the wiki page link above describes how to include these various Galaxy utilities.

Even Galaxy tools fall into various categories. For example, some are very simple, requiring no 3rd party tool dependencies and the tool form does not use dynamically generated select lists. These generally only require a script and an XML file. However, more complex Galaxy tools may require additional supporting content to be included in the repository (e.g., a tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are building, I can steer you to the wiki pages that provide information about those specific utilities.

Thanks!

Greg Von Kuster

On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:

Hi All,

We are experimenting with local toolsheds for tool maintainability. On the old galaxy wiki I can remember there was a short tutorial or small description of the minimal requirements of a tool to be submitted to the toolshed. Actually we submitted some. However we seem unable to retrieve the proper info from the updated wiki. We did find info on single tools or suites, or more special cases, but a simple example/list of how and what to include in a repository is missing (at least we cannot find it....might be an issue of wrong key words)..

Anyone has an idea where to find such a document?

Thanks Alex

___________________________________________________________ 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:

http://lists.bx.psu.edu/