Re: [galaxy-dev] provide a field to upload a file as part of tool input

I figured out the optional part (RTFM to myself) On Fri, Aug 5, 2016 at 6:54 PM, Ryan G wrote: > Hi all - I have a custom tool that can optionally take a file as input. > > Right now, users have to upload the file into their history, then select > the file when

[galaxy-dev] provide a field to upload a file as part of tool input

Hi all - I have a custom tool that can optionally take a file as input. Right now, users have to upload the file into their history, then select the file when running the tool. Is there a way to let the user select a file local on their computer as input to the tool, then when run, the file is

Re: [galaxy-dev] Parameter Storing in Database

You mean the stuff for the tool-data tables? As I understand it, it is loaded in: lib/galaxy/tools/data/__init__.py There's a ToolDataTableManager and a TabularToolDataTable (with associated TabularToolDataField). Peter On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu <

[galaxy-dev] Parameter Storing in Database

Would anyone be able to tell me in what file the storing of tool parameters into the database occurs? Thanks! Katherine ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this

Re: [galaxy-dev] Command line building

Check out https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/command_factory.py Let me know if this wasn't what you were looking for. -Dannon On Fri, Aug 5, 2016 at 10:49 AM Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Within the galaxy app itself, does anyone

Re: [galaxy-dev] Retrieving bam index file for visualization outside of Galaxy

Hi Scott, This isn't currently exposed through the API, but I'm working on implementing it at https://github.com/galaxyproject/galaxy/pull/2741, if you'd like to test it. -Dannon On Thu, Aug 4, 2016 at 10:38 AM Ouellette, Scott < scott_ouelle...@hms.harvard.edu> wrote: > Hi all, > > I have a

Re: [galaxy-dev] conversion issue

Yes I did. All tools are installed and I see no error message. Philipp ---Philipp on the road--- Am 05.08.2016 um 15:31 schrieb Peter Cock >: Its sounds like bedGraphToBigWig has not been installed.

Re: [galaxy-dev] uploading multi-file archives and creation of potentially large collections

Hi Stephan, I will only answer about uploading zip files. Since the release_16.04, a zip datatype is integrated within the Galaxy distribution. But without any sniffer, so your users will have to select, before the upload, the zip datatype manually. I also want to write this kind of tool which