[galaxy-dev] Importing Historys in other Galaxy instances

Hi everybody, I got another question concerning our own Galaxy instance. We are trying to import Histories from the public Galaxy server via Export to file (in the public-Galaxy-account), saving the export-Link and Import from File in the account on our local system. But the histories never

[galaxy-dev] Exporting histories through API

Hello there As the subject hints, I am trying to export histories through the API. Doing it through the web interface is a breeze, but has it been implemented in the API yet? I could not find anything about it in the examples or by searching the web/this list. I am planning to only use Galaxy

Re: [galaxy-dev] Data Retention Policies

On Oct 24, 2011, at 2:57 AM, Peter Cock wrote: On Mon, Oct 24, 2011 at 4:53 AM, John Chilton chil...@msi.umn.edu wrote: Hello All, This is more of a general policy question. The head of our Research Informatics Support Systems group here at the University of Minnesota wants to know how

Re: [galaxy-dev] Few possible galaxy bugs ?

On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC) michael.burr...@nbi.ac.uk wrote: Good afternoon Peter, Thank you for your rapid response, My understanding is that this tool was installed locally from the tool shed, unfortunately I do not know if it was working before the update was

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

Any more thought on how to accomplish this without my current hack? Ideally it would be great if this feature could become part of galaxy-central. This is a feature that we would really like to implement so that our reports can link to the output files. Thanks, Ilya -Original

Re: [galaxy-dev] upload error in the local instance of galaxy

Brad Langhorst wrote: On 10/19/11 3:09 AM, Amit Anand a...@tll.org.sg wrote: Hi, I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to

Re: [galaxy-dev] FW: one error while installing galaxy

Li, Jilong (MU-Student) wrote: Hi, When I installed galaxy, one error message appeared, which said that ImportError: No module named distutils.util Fetch failed. Could you tell me how to solve this problem? Thank you very much! Hi Jilong, Since this is a question regarding a local

Re: [galaxy-dev] Job output not returned from cluster

Joseph Hargitai wrote: Nate, this error is intermittent. You resubmit the same job twice or three time and then it works. Once we are over the midterm exams - which use galaxy - we will try to switch the filesystem from autofs to hard mount. We suspect this to be the issue. Ah, I

Re: [galaxy-dev] Problem uploading sorted BAM files

Stephen Eacker wrote: Hello, I'm trying to upload a 600MB BAM file to my local instance of Galaxy but the upload fails. I tried to follow a thread on this topic archived on osdir.com but could not find if the issue was resolved. My BAM file has been previously been sorted and

[galaxy-dev] Broad IGV

I saw some posts and a commit which allows one to use broad IGV within galaxy but I do not see a tool, a link, or an option. Can someone explain how to set that up? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work:

Re: [galaxy-dev] Broad IGV

Hi Ilya, In datatypes_conf.xml, under the bam datatype uncomment out the display application for igv/bam (display file=igv/bam.xml /). Links will then appear for bam history items. Thanks for using Galaxy, Dan On Oct 24, 2011, at 5:50 PM, Chorny, Ilya wrote: I saw some posts and a commit