For the simplest case, start with the tools/rgenetics/rgFastQC tool - it doesn't need a subclass but uses the Html datatype files_path as a simple multiple file bucket. Once you've got that all figured out, check out the rgenetics datatypes (eg pbed) subclassed from Html defined in lib/galaxy/datatypes/genetics and the tools that use it (eg TDT or CaCo tools) in tools/rgenetics for more complex hackery keeping related files needed by plink together.
On Fri, Jan 4, 2013 at 9:50 AM, <neil.burd...@csiro.au> wrote: > Thanks for the help Ross.**** > > ** ** > > Any chance you can point me to the examples you mentioned?**** > > ** ** > > Thanks again**** > > Neil**** > > ** ** > > *From:* Ross [mailto:ross.laza...@gmail.com] > *Sent:* Friday, 4 January 2013 8:35 AM > > *To:* Burdett, Neil (ICT Centre, Herston - RBWH) > *Cc:* galaxy-user > *Subject:* Re: [galaxy-user] Upload files from filesystem paths**** > > ** ** > > Hi, Neal,**** > > Thanks - that sounds interesting. Like I said, composite datatypes are > designed to manage collections of related files as a unit and this sounds > like a potential use case. There are lots of tools and lots of code that > can serve as examples but it's definitely not trivial because you will > almost certainly be subclassing the Html data class and writing methods to > manage those related files (ie extending the guts of Galaxy) and your tools > will all need to know how to deal with the managed structure when they get > one as an input. **** > > ** ** > > You may need to find or build up a programmer with some relevant Galaxy > composite datatype experience. There is some documentation but it's not > extensive or transparent. **** > > ** ** > > Good luck.**** > > ** ** > > On Fri, Jan 4, 2013 at 9:19 AM, <neil.burd...@csiro.au> wrote:**** > > Hi Ross,**** > > I don’t know of any tools that work in the way I want, but > I’m not an expert on tools within Galaxy. Essentially the data in the > directories will be fixed. We run a tool from Galaxy that generates some > output data, this data then “checks” the data located under the directories > I am trying to upload to Galaxy. There will probably be around 20 > directories, and the data produced would then search these directories > looking for “a closest match” once located it would use the remaining files > in the directory to complete the process.**** > > **** > > So for example, the application is segmenting an image, so a part of the > image is the output. This is compared with files in the uploaded > directories and a file in a particular directory is chosen (as the closest > match) then the remaining files in the directory are then used to complete > the process.**** > > **** > > Does that make sense? There would be around 20 files in each directory.*** > * > > **** > > Thanks**** > > Neil**** > > **** > > *From:* Ross [mailto:ross.laza...@gmail.com] > *Sent:* Thursday, 3 January 2013 2:24 PM**** > > > *To:* Burdett, Neil (ICT Centre, Herston - RBWH) > *Cc:* galaxy-user > *Subject:* Re: [galaxy-user] Upload files from filesystem paths**** > > **** > > Neil, **** > > It would help if you could point to an existing tool that works the way > you want. I don't know of any that deal with arbitrary nested directories > containing arbitrary files. A new composite datatype could impose a > structure that a tool could be written to deal with (eg the pbed datatype > used in some rgenetics tools) but arbitrary data structures are not going > to be possible AFAIK. You're unlikely to get useful help without a much > more complete and clear explanation of the problem.**** > > **** > > **** > > On Thu, Jan 3, 2013 at 1:50 PM, <neil.burd...@csiro.au> wrote:**** > > Hi Ross, > I think I need to clarify. I have a file in > /home/galaxy/data-test/dir1/dir2/somefile.txt > > Under the "Upload files from filesystem paths", In the "path to upload" > window I paste "/home/galaxy/data-test". This then puts the "somefile.txt" > in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I > elected to keep the directory structure. I can see this if I navigate > through the "shared data" tab but where is this information stored under > the galaxt-dist structure. As my application needs to have the directory > structure kept, so need to access it from the xml/command line > > I thought it might have been something like: > /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. > But this is not the case rather > /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no > directory structure. So how can I access this information from the xml > files in the tools directory? > > Thanks > Neil > ________________________________________ > From: Ross [ross.laza...@gmail.com] > Sent: Wednesday, January 02, 2013 4:43 PM > To: Burdett, Neil (ICT Centre, Herston - RBWH) > Cc: galaxy-user > Subject: Re: [galaxy-user] Upload files from filesystem paths**** > > > Try importing those library files to the history where you want them - > browse the Galaxy 'shared data' tab to where you uploaded them.**** > > On Wed, Jan 2, 2013 at 11:39 AM, <neil.burd...@csiro.au<mailto: > neil.burd...@csiro.au>> wrote: > Hi, > I have a local galaxy installation. > > I've created a data library, selected "Upload files from filesystem > paths", pasted a path in the "path to upload" window, and I've selected to > preserve the directory structure". And the files get imported. > > How do I now access these files from my application? I don't want to > import them into the history as then they lose the directory structure. I > can't see where they are physically under the galaxy-dist structure > > Thanks for any help > > Neil**** > > **** > > ** ** >
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