Hi Yvan, > Hi Lance, Björn, Dan > > We are several scientists working on metagenomics in France and at a > previous GUGGO (western France User Group) meeting, we mention the > fact to "benchmark" our Galaxy pipelines. One is using new Qiime > tools integration, one Mothur and the last one, the recently > developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline > using Swarm. We already have had some exchanges with Björn concerning > metagenomics flavours on Docker, and I think it will be particularly > interesting to exchange one with each other. The Qiime integration > was started in march by colleagues from Brest Ifremer centre. I was > just trying to install and test FROGS from Toulouse and Jouy-en-Josas > INRA labs. If they are not on the list, I can contact them.
Please do so. This is great to know. Please also consider to join our hackathon: https://github.com/galaxyproject/tools-iuc/issues/299 We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :) Thanks, Bjoern > All the best, > > Yvan > > ----- Mail original ----- >> De: "Björn Grüning" <bjoern.gruen...@gmail.com> À: "Lance Parsons" >> <lpars...@princeton.edu>, "Daniel Blankenberg" <d...@bx.psu.edu> Cc: >> "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: >> Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME >> tools for Galaxy (WIP, call for collaborators) >> >> 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. To manage your subscriptions to this and other >>> Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> ___________________________________________________________ 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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