For the list sake - I think we figured this out and IRC and it had to do with having two versions of Galaxy installed on the same machine. Alexander - let me know if this issue is not resolved.
-John On Mon, Jun 15, 2015 at 4:02 PM, Alexander Vowinkel <vowinkel.alexan...@gmail.com> wrote: > Thank you for this detailed descriptions! > > I already have a followup question. > I'm working on Galaxy Cloudman: >> >> Galaxy is at revision: 93cda3eb81 (master branch) from 11 Jun 2015) > > > But I just can find "Build dataset pair|list", not "List of Dataset Pairs" > like > in the video. At what version is that implemented? > > Best, > Alexander > > 2015-06-15 10:17 GMT-05:00 John Chilton <jmchil...@gmail.com>: >> >> On Wed, Jun 10, 2015 at 4:04 PM, Alexander Vowinkel >> <vowinkel.alexan...@gmail.com> wrote: >> > Hi Folks, >> > >> > thank you so far for the previous help. I got much further. >> > Now I'm stuck with data collections. >> > >> > Because this is quite a list, I appreciate also answers to parts of my >> > questions ;) >> > >> > I have two issues: >> > A) manual definition of data collections (any type) by user and/or admin >> > B) definition of data collections as input/output of a tool and inside a >> > workflow >> > >> > >> > A) manual >> > Basically I would like to create >> > i) a list of fastq files (unpaired) >> > ii) a paired set of two fastq files >> > iii) a list of each two paired fastq files >> > >> > How can I do that? >> > By using the web app? As user? As admin? >> > By working via ssh on the server? >> >> So each of these got much easier/more robust with the most recent release. >> >> For the user perspective - for any of these options you will want to >> load the fastq files into a history, open the manage multiple datasets >> option >> (https://wiki.galaxyproject.org/Histories#Managing_Multiple_Datasets_Easily), >> select the datasets, and then choose the list type from the menu. Each >> will cause a widget to pop up allowing you to group the datasets (into >> a list, a pair, or a list of pairs depending on your selection). >> >> The most complicated option is the list of pairs - this option is >> demonstrated in a the first video in Anton's recent NGS 101 - >> Reference-based RNA-seq series >> (https://vimeo.com/channels/884356/128265983). More information at >> https://wiki.galaxyproject.org/Learn/GalaxyNGS101. >> >> For all user-centric scenarios - you will need to get the plain >> datasets into a history first. FTP upload for instance doesn't support >> creating collections directly - you can import datasets and then >> create them. Likewise - data libraries do not currently support >> dataset collections. I believe there are Trello cards for both of >> these issues. >> >> For admins - there is a dataset collection API - I can point you at >> examples if you want - but this doesn't seem to be your interest. >> >> > >> > >> > B) in tool/workflow >> > Here I also have different approaches I would like to realize: >> > i) use a collection as input for a tool >> > ii) create a collection as output of a tool >> > ii.1) from known # of output parameters >> > ii.2) from unknown # of output parameters >> > >> > For these things I was trying to find some tools in toolshed to see how >> > they >> > do it, but I couldn't quite adopt it. >> >> I would look in the following directory instead of the tool shed - >> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools. >> These are the tools used to drive the testing of the collections >> implementation and contain some very stripped down examples of what is >> possible. >> >> > >> > i) use a collection as input for a tool >> > this is good documented - realizable by type="data_collection" and the >> > collection_type. >> > Unfortunately I can't test this because I can't create a collection so >> > far >> > ;) - see A >> >> Indeed :). Here some good examples are like the tools in the RNA-seq >> pipeline - Tophat, Bowtie2, etc.... >> >> > >> > ii) create a collection as output of a tool >> > Here it gets blurry for me. >> >> So one can get very far without ever creating an output from a tool >> explicitly. I contend most of the time - if you have a list of bam >> files and you want to create another list of bam files - you just want >> to map some operation over them. This is demonstrated in that RNA-seq >> outline - and talked about in a more theoretical way in my GCC talk >> from last year http://bit.ly/gcc2014workflows. >> >> There are definitely cases when you want to explicitly create >> collections though - the current best documentation on this is going >> to be the pull request that added them - not the implementation but >> the description which actually lays out these same categories and how >> to handle them with explicit complete examples. >> >> https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset >> >> Hopefully this helps - please follow up with additional questions as >> you have them. I am keen to see more developers leveraging dataset >> collections. >> >> Thanks a bunch. >> -John >> >> > >> > ii.1) from known # of output parameters >> > Here I didn't find a tool. I just thought, it might be a simpler case >> > than >> > ii.2 and >> > good to understand the concept. >> > I would be glad if someone could explain the way(s) to do this. >> > >> > ii.2) from unknown # of output parameters >> > For this I found barcode splitter tools (also from devteam) that have >> > different approaches. >> > But. Their output (defined in xml) is only some report file. >> > The output files seem to be fed into the history. >> > And here I don't know how to get hands on these files when I want to use >> > them to feed them into the next step during a workflow. >> > >> > Help highly appreciated! >> > >> > Thanks! >> > Alexander >> > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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