[galaxy-dev] where can I find galaxy code documentation?

2012-04-16 Thread Eli Reuveni
From: Eli Reuveni Sent: Monday, April 16, 2012 9:13 AM To: 'galaxy-dev@lists.bx.psu.edu' Subject: where can I find galaxy code documentation? Hi, I have a local galaxy instance in my institute and have few basic questions: 1) I need to enable galaxy to upload large files from the local

[galaxy-dev] Workflow Tags

2012-04-16 Thread Frank Sørensen
Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of tags in the tag list doubles, and thus rapidly grows towards infinity, and

[galaxy-dev] Just wanted to say...

2012-04-16 Thread Louise-Amélie Schmitt
I love the improvements you recently made to the web interface layout in galaxy-central, it's really neat! Collapsing the margins and making everything smoother makes the interface really easier to read. Thanks for the hard work, as always, L-A

Re: [galaxy-dev] Workflow Tags

2012-04-16 Thread Peter Cock
On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensen frank.soren...@ki.au.dk wrote: Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of

Re: [galaxy-dev] Workflow Tags

2012-04-16 Thread Frank Sørensen
Hi Peter, Thanks for the prompt answer. I'm not quite sure which release I'm running. But I'll try to update and see if the problem is solved. Kind Regards Frank Den 16-04-2012 09:54, Peter Cock skrev: On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensenfrank.soren...@ki.au.dk wrote: Hi

[galaxy-dev] This link may not be followed from within Galaxy.

2012-04-16 Thread Eli Reuveni
Hi, I am getting the error This link may not be followed from within Galaxy. When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Best ___

Re: [galaxy-dev] Issues with local instance of toolshed?

2012-04-16 Thread Greg Von Kuster
Hi Amanda, I'll need to see your paster log to be able to help on this one. You can view it using tail -f community_webapp.log (without the quotes) from your Galaxy install directory. Can you respond back with the content? Thanks, Greg Von Kuster On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo

[galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

2012-04-16 Thread Hans-Rudolf Hotz
Hi We are in the process of migrating our Galaxy servers to the current March 12, 2012 release ('6799:40f1816d6857'). We have encountered two issues, which I guess are related: If I restart the server, I get: galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database version 93

Re: [galaxy-dev] Workflow import error

2012-04-16 Thread Greg Von Kuster
Hi Rob, When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? Thanks, Greg Von

Re: [galaxy-dev] GCC2012 Abstract Submission Deadline is April 16, one week from today.

2012-04-16 Thread Dave Clements
Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is TODAY. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, Dave C On Mon, Apr 9, 2012 at 2:03 PM, Dave Clements cleme...@galaxyproject.orgwrote:

Re: [galaxy-dev] where can I find galaxy code documentation?

2012-04-16 Thread Nate Coraor
Thanks for the example, Frank. You can upload to data libraries directly from the local filesystem. The relevant documentation is here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Eli, with respect to the question about modifying galaxy-dist/lib:

Re: [galaxy-dev] This link may not be followed from within Galaxy.

2012-04-16 Thread Nate Coraor
On Apr 16, 2012, at 7:13 AM, Eli Reuveni wrote: Hi, I am getting the error “This link may not be followed from within Galaxy.” When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Hi

[galaxy-dev] Error copying files from job_working_directory

2012-04-16 Thread Jose Navas
Hello, I've integrated a tool into my Galaxy instance, but when I run the tool I get this error: galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying /home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous to

[galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

2012-04-16 Thread zhengqiu cai
Hi All, I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 336, in finish_job

Re: [galaxy-dev] Workflow import error

2012-04-16 Thread Greg Von Kuster
Hi Robert, I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow

Re: [galaxy-dev] Error copying files from job_working_directory

2012-04-16 Thread Jose Navas
Hi everybody, I was searching through the Galaxy code and I find the solution: the function responsible for copying files is using shutil.copy function, which only allows copy files. I've modified this function to use shutil.copytree in case of file_name is a directory. I can send you the code

Re: [galaxy-dev] Workflow import error

2012-04-16 Thread Dannon Baker
Robert, It sounds like you're experiencing two separate problems to me. Let's isolating the problem to just the FastQC tool install, first, and move on from there. There is a FastQC tool in your toolbar, and execution results in the error you describe in the previous email of 'Fastq failed.