Hi Lance, I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :) Thanks, Bjoern Am 06.10.2015 um 20:33 schrieb Lance Parsons: > I agree that it would be very nice to get the data flowing between each > of the tools and to be able to mix/match with other tools. That is an > area of Galaxy tool-dev that I'm less familiar with, so any help would > be greatly appreciated. > > As for the manual massaging, I agree, however, at this point I'm really > hoping that the changes between Qiime versions are manageable, esp. once > we have the data types and basic framework of the tools down. > > Along that front, I would very much like to get something usable (at > least for some specific workflows) done sooner rather than later, then > be able to iterate, adding new tools, datatypes, etc. as we move > forward. Does that sound reasonable? I love the idea of a Metagenomics > toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One > thing I would like to do soon then, would be to define some > functionality for the first round. What would be very helpful would be > if you, Bjoern, etc. could help make sure the first round lays the > proper groundwork so I/we don't have to redo things for later > iterations, but we can build on a solid foundation. > > Thanks so much for the input, help, etc. It is very much appreciated. > > - Lance > >> Daniel Blankenberg <mailto:d...@bx.psu.edu> >> October 6, 2015 at 10:21 AM >> Hi Lance, >> >> I looked at this a bit ago and had similar concerns, particularly with >> the outputs and inputs not being well-defined. In addition to the >> output tar ball —> local, extract —> upload not being great, as you >> mention, the input datatypes, etc, could use some work — in the very >> least, we should definitely create a nice biom datatype and have some >> converters available (import and export). >> >> Definitely worth spending some extra time to make sure that we have >> the data flowing well between each of the different parts/tools, and >> even better to make sure that its done in a way that allows mixing and >> matching with other non-qiime tools. >> >> >> One thing that we want to avoid is large amounts of manual massaging >> of the automatically generated xml; fixing things up once might not be >> too bad, but having to do it with each new tool version can be >> “frustrating". Although perhaps having a good starting point and only >> needing to manually modify for any updates could be good enough (I’m >> not very familiar with the extent of typical changes between qiime >> versions to make a call on how much changes). >> >> >> >> >> Dan >> >> (resending since I received a message bounce from list) >> >> >> >> Daniel Blankenberg <mailto:d...@bx.psu.edu> >> October 6, 2015 at 9:59 AM >> Hi Lance, >> >> I looked at this a bit ago and had similar concerns, particularly with >> the outputs and inputs not being well-defined. In addition to the >> output tar ball —> local, extract —> upload not being great, as you >> mention, the input datatypes, etc, could use some work — in the very >> least, we should definitely create a nice biom datatype and have some >> converters available (import and export). >> >> Definitely worth spending some extra time to make sure that we have >> the data flowing well between each of the different parts/tools, and >> even better to make sure that its done in a way that allows mixing and >> matching with other non-qiime tools. >> >> >> One thing that we want to avoid is large amounts of manual massaging >> of the automatically generated xml; fixing things up once might not be >> too bad, but having to do it with each new tool version can be >> “frustrating". Although perhaps having a good starting point and only >> needing to manually modify for any updates could be good enough (I’m >> not very familiar with the extent of typical changes between qiime >> versions to make a call on how much changes). >> >> >> >> >> Dan >> >> >> >> Lance Parsons <mailto:lpars...@princeton.edu> >> October 5, 2015 at 5:26 PM >> I was recently asked if I could provide a QIIME analysis pipeline for >> 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/). >> >> I did a bit of looking around for existing Galaxy wrappers and found >> an application that generates the wrappers for QIIME scripts for >> Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well >> written application that does a great job of wrapping the QIIME >> scripts for Galaxy. However, there are a few things about it that >> don't quite fit my needs. >> >> 1. The tools output tgz files of all of the output files. This means >> that to execute a pipeline, the user would have to download the tgz >> files, untar, and then upload whichever file(s) are needed for the >> next step. >> 2. There is no toolshed repository to install the dependencies for >> these tools, making it a tricky for administrators to automate and >> also maintain various versions of QIIME going forward. >> 3. There are no toolshed versions of the tools themselves, which also >> makes installation and integration a bit tricky and makes it hard to >> me to create and manage updates, fixes, tweaks, etc. There are also no >> tests, etc. >> >> For these reasons I decided to investigate the feasibility of using >> the generated wrappers as a basis for a "toolshed" version of QIIME. >> If anyone is interested in helping, or has suggestions, or is working >> on something related, I'd be very happy to collaborate. >> >> The repository for the WIP is at >> https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. >> There is also a package on the testtoolshed as well as a first pass at >> package_qiime_1_9_1 >> (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1_9_1). >> >> > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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