Re: [galaxy-dev] Tools that make datasets

Just a quick check - did you refresh your history to confirm that the dataset *is* empty? We had the same thing at SANBI but it turns out that Galaxy creates an empty output collection and then only populates it sometime after job completion (this is a know UI bug). See:

Re: [galaxy-dev] Tools that make datasets

Thanks Peter, I did see that proviso somewhere but no, refreshing doesn't help. That page was one of those that I referred to getting to this point. Steve On 20 October 2015 at 18:33, Peter van Heusden wrote: > Just a quick check - did you refresh your history to confirm

[galaxy-dev] Developing package wrappers

Hi, I am afraid that I might be overlooking something obvious but... I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For that effect I am designing a few package wrappers. My problem is to understand the best practice to develop wrappers for dependencies of external tools.

Re: [galaxy-dev] Tools that make datasets

I suspect that the problem might be in the then. I'm not an export on this, but "__name_and_ext__" turns into the regexp r"(?P.*)\.(?P[^\.]+)?" in lib/galaxy/tools/parameters/output_collect.py, and is used by the DatasetCollector (line 358). This looks like it should match the filenames you're

Re: [galaxy-dev] Tools that make datasets

Yes, I'm sure that's where the problem lies. Writing out to the current directory doesn't work. The files get written to 'job_working_directory/000/1/' but if I run the Upload File tool the result is placed in 'files/000/'. I think I need to work out where to write the files, I found some

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

Hello, I am sorry but I have really no experience with setting up the Apache web server so I am not really sure how to do that. Can you please help me out with it? My apache configuration file is in /etc/httpd/conf/ directory and there are no directories such as /sites-available/ or

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

Hi, I'm afraid it won't be easy to reproduce my problem with a clean galaxy install. I think it has to do with the history of the instance, a lot of back and forth on the tool installations and also lot's of failed installations (due to my environment or network issues). Investigating the

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

Hi, If you have a line in your Apache conf like "Listen 80" change to "Listen 8081" > On 20 Oct 2015, at 21:00, Makis Ladoukakis wrote: > > Hello, > > I am sorry but I have really no experience with setting up the Apache web > server so I am not really sure how to

Re: [galaxy-dev] Developing package wrappers

Hi Tiago, for simple tool_dependencies you can use the new planemo depbash command from Peter: https://github.com/galaxyproject/planemo/pull/310 For more complicated once I recommend to use the TTS for the time being. You can create the initial repository install from it and change your

[galaxy-dev] Tools that make datasets

Hi all, I'm trying to understand how to write a tool that generates a dataset rather than a single output file. I've tried following all of the examples but I'm stuck, so I thought I would distil down the simplest example I could write and ask for help here. So here's my example:

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

Sorry to hijack the thread, but I think the issue that Sarah has described could be related to https://github.com/galaxyproject/galaxy/issues/667. (I know it's not exactly the same, but chances are we fix this, we automatically fix Sarah's issue.) There is also an example to reproduce

Re: [galaxy-dev] Developing package wrappers

On Tue, 20 Oct 2015 14:48:08 +0200 Bjoern Gruening wrote: > Hi Tiago, > > for simple tool_dependencies you can use the new planemo depbash > command from Peter: > https://github.com/galaxyproject/planemo/pull/310 Gosh, this is exactly what the doctor ordered. Thanks

Re: [galaxy-dev] Tools that make datasets

Ah, thankyou, yes, I can now get results by using patterns to match the output. I used your example but prepend 'simple' to the filename and then searches for that with: this solves the problem for the sample script but not generally since in general I can't predict the filenames that will be

Re: [galaxy-dev] Developing package wrappers

On Tue, Oct 20, 2015 at 10:01 AM, Tiago Rodrigues Antao wrote: > Hi, > > I am afraid that I might be overlooking something obvious but... > > I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For > that effect I am designing a few package wrappers. My problem is

Re: [galaxy-dev] Tools that make datasets

I poked around at your tool XML and the code a bit and the problem is directory="$job_name". Galaxy expects to collect files from the job's working directory - basically the current working directory the job runs in. The directory= argument doesn't have variables expanded as far as I can tell. In