An Idea For Sharing Tools

Question: An Idea For Sharing Tools

10.0 years ago by

James Casbon • 370 wrote:

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

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modified 10.0 years ago by James Taylor • 70 • written 10.0 years ago by James Casbon • 370

10.0 years ago by

James Taylor • 70

James Taylor • 70 wrote:

This is something we're very interested in facilitating. For the long term, we're hoping to provide a structured / wiki environment for people to share tools and suites of tools, as well as providing more support in the application for adding self-contained tool suites to a Galaxy instance, injecting local configuration into tools and tool suites, et cetera. However, we'd also be very happy to see the mailing list used for this at the moment, and might even be able to open up a section of the wiki for users to list the tools they are making available. This is much trickier. We have to carefully consider two things when including a tool in the "default" set. 1) Quality -- we want to integrate the best possible tools for specific tasks, since one a tool starts being used, and has workflows and histories that depend on it, it is difficult to change substantially or replace. Sharing tools helps us here: if the user community comes to a consensus that a tool is useful, that is a good argument for including it upstream. 2) Security -- this is probably an even bigger concern. Tools like the "awk" tool are pretty dangerous. Until / unless the Galaxy framework can enforce complete tool isolation we definitely don't want to include a tool like this in the main distribution. -- jt James Taylor Assistant Professor Department of Biology Department of Mathematics & Computer Science Emory University

ADD COMMENT • link written 10.0 years ago by James Taylor • 70

Hello all, James Taylor wrote, On 12/03/2008 12:13 PM: Just a quick note about the AWK and SED tools: I've patched both AWK and SED and disabled the 'dangerous' parts. (this patch is pending acceptance by the awk/sed maintainers.) With this patch, both programs can operate ONLY on the input file given by galaxy, and can not execute programs or read files or write files other than what Galaxy framework has given the awk/sed program. I'll be glad to share these tools. -Gordon.

ADD REPLY • link written 10.0 years ago by Assaf Gordon • 320

2008/12/3 James Taylor <james.taylor@emory.edu>: Can we send attachments to the mailing list? I would have thought the easiest way would be to give some trac permissions (ticket create, wiki edit) to list members. It's easier to work with than a mailing list. I would also prefer filing bugs on trac than mailing them to a list. All in all, why not allow others to use your issue tracking and wiki? Requires little effort from you except handing out accounts. cheers, James

ADD REPLY • link written 9.9 years ago by James Casbon • 370

Hi James, We're in the process of transitioning from trac to bitbucket. Our bitbucket project can be found here: http://bitbucket.org/galaxy/galaxy-central/ Bugs and patches can be submitted directly through the ticket interface there. Please note that the best place for usability questions is still galaxy-user. In addition, installation/configuration problems, tool contributions, ideas, discussion, etc. are still appropriate topics for galaxy-dev. --nate

ADD REPLY • link written 9.5 years ago by Nate Coraor ♦ 3.2k

10.0 years ago by

Peter Rice • 30

Peter Rice • 30 wrote:

We would be happy to help. Maybe we can cover maintenance of EMBOSS tools too? Peter Rice EBI

ADD COMMENT • link written 10.0 years ago by Peter Rice • 30

Would a wiki-like environment be an alternative way? People could then host the actual code as they see fit and supply download instructions. If a group wants to collaborate, they can open their VCS of choice to the respective collaborators. Sean

ADD REPLY • link written 10.0 years ago by Sean Davis • 220

10.0 years ago by

Giovanni Marco Dall'Olio • 10

Giovanni Marco Dall'Olio • 10 wrote:

Hi, I would suggest you to put your scripts on github or on a similar web repository, and then share the link with all the people you want. If you don't want to use a commercial service (it is free, anyway), I think the best option is to put a repository using trac. -- My blog on bioinformatics (now in English): http://bioinfoblog.it

ADD COMMENT • link written 10.0 years ago by Giovanni Marco Dall'Olio • 10

2008/12/3 Giovanni Marco Dall'Olio <dalloliogm@gmail.com>: Well, I certainly don't want this thread to be about which VCS is best, I think that is covered elsewhere ;) If anything, mercurial is the sensible option because that allows you to work with the existing source tree. A better way to approach this might be to ask what tools you have added, or would be interested in, so we can see what overlap there is. So, I'll start. I have added: exonerate, restriction mapping, gnu tool chain (sort, uniq, cut, etc) would be interested in: 454 tools (sfffile, etc), interaction with pygr (woudl be difficult), hapmap. I suppose once workflows are stable, a way to share those would be good. There is that website somewhere for doing this, but I can't remember the name right now. cheers, James

ADD REPLY • link written 10.0 years ago by James Casbon • 370

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