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

2016-08-05 Thread Ryan G
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 running the tool. > > Is there

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

2016-08-05 Thread Ryan G
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 up

Re: [galaxy-dev] Parameter Storing in Database

2016-08-05 Thread Peter van Heusden
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 < katherine.beaulieu...@gmai

[galaxy-dev] Parameter Storing in Database

2016-08-05 Thread Katherine Beaulieu
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 and

Re: [galaxy-dev] Command line building

2016-08-05 Thread Katherine Beaulieu
On Fri, Aug 5, 2016 at 11:20 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Thats perfect thanks so much!:) > > On Fri, Aug 5, 2016 at 11:18 AM, Dannon Baker > wrote: > >> Got it, misunderstood your interest. You want this, see the >> fill_template usage in this method: >> ht

Re: [galaxy-dev] Command line building

2016-08-05 Thread Dannon Baker
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 kn

[galaxy-dev] Command line building

2016-08-05 Thread Katherine Beaulieu
Within the galaxy app itself, does anyone know where the command line is being built? Thanks! Katherine ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy li

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .
Hi Peter, it looks like samtools is not functional ==> /home/galaxy/logs/uwsgi.log <== galaxy.tools DEBUG 2016-08-05 14:25:25,686 Validated and populated state for tool request (52.679 ms) galaxy.tools.actions INFO 2016-08-05 14:25:25,754 Handled output named out for tool toolshed

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

2016-08-05 Thread Dannon Baker
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 us

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Peter Cock
I think you will need to look at the Galaxy logs for some clues about if the dependencies are being found or not. The simple "hack" is to install them on the $PATH manually, which would be the practical solution if this is urgent. Peter On Fri, Aug 5, 2016 at 3:09 PM, Rathert, Philipp, Dr. wrote

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .
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 mailto:p.j.a.c...@googlemail.com> >: Its sounds like bedGraphToBigWig has not been installed. https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwi

Re: [galaxy-dev] conversion issue

2016-08-05 Thread Peter Cock
Its sounds like bedGraphToBigWig has not been installed. https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/ The README says: > Ensure the following command line tools are on the system path: > > pysam - Python interface to samtools (http://code.google.com/p/pysam/) > genomeCoverageB

[galaxy-dev] conversion issue

2016-08-05 Thread Rathert , Philipp , Dr .
Dear All, I get the following errors when I try to Convert BAM to BigWig Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in main(*args, **kwargs) Fil

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

2016-08-05 Thread Björn Grüning
Hi Stephan and Gildas, I think a tool is a nice addition. Archives can be arbitrary complex and nested so a tool would make perfect sense. If this tools is working well and we know which features we need and how they should be displayed to the user it more easy to move these kind of functionality

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

2016-08-05 Thread Gildas Le Corguillé
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