[galaxy-dev] Question about compressed files

Hi all, My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he

[galaxy-dev] Liftover tool installation woes

Hi Everyone, I installed a local instance of galaxy and some tools using the command line, and for some reason liftover will work in the command line but won't work in galaxy. Here's what I've done so far: - Downloaded liftover standalone executable from the tool-dependencies page in the Gwiki.

[galaxy-dev] how to create a new tag in tool_xml_file of galaxy

Hi, I am using my local instance of galaxy . I want to create a tag which will open an new window in galaxy. How can i create a new tag in tool_xml_file ? for this any modification is required in any file of galaxy ? Regards shashi --

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

Thanks Dannon and Bjorn for the assistance. I followed Dannon's suggestion and that fixed my issue. Thanks, Iry On 7/3/12 1:15 PM, "Dannon Baker" wrote: >It looks like what happened is that you've updated the instance that was >originally connected to this database from galaxy-central at some

Re: [galaxy-dev] Display IGV link within history bam items?

Resolved! In fact i forgot to set the database infomration (hg18) in the bam item. so Now I can see the display igv link :) 2012/7/3 Chebbi Mohamed Amine > Hi ! > I'am trying to set IGV as a display application in Galaxy. So I have addedin > datatypes_conf.xml, under the bam datatype the displa

[galaxy-dev] Display IGV link within history bam items?

Hi ! I'am trying to set IGV as a display application in Galaxy. So I have addedin datatypes_conf.xml, under the bam datatype the display application for igv/bam (). However the Links dose not appear in bam history items. I see only " display in IGB Local

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

Hi Iry, > > Exception: Your database has version '101' but this code expects > version '97'. Please backup your database and then migrate the schema > by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. > Removing PID file runner0.pid Your galaxy version seems to be older than

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

It looks like what happened is that you've updated the instance that was originally connected to this database from galaxy-central at some point recently. The current tip of galaxy-central is at database version 103. The first two options that come to mind are: 1) Hook a fresh galaxy-central

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

I am still experiencing issues getting my galaxy server to start since the upgrade. The logs are all getting this type of error: galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log python path is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-lin

[galaxy-dev] bug in transferring files in Galaxy to the UCSC browser

Hi, For some time now, we have found that wig files on the Penn State Galaxy cannot be transferred into the UCSC browser via the Galaxy URL. We receive the error: " Error Unrecognized format line 2 of https://main.g2.bx.psu.edu/datasets/329241/display/: (note: chrom names are case sensitive)".

Re: [galaxy-dev] problems installing mothur via toolshed

Hello Matthias, The setting for tool_path is likely not the culprit. Your success in being able to install the repository is most likely due to the small fix I committed to the tool shed yesterday afternoon that affected the contents of this particular tool suite. You should be running the

Re: [galaxy-dev] problems installing mothur via toolshed

Hi Greg, 1. changeset: 7284:87be4c8d7f7f 2. 3. yes, the latest Solved! I noticed that my tool_path was different from yours. After setting it to ../shed_tools it installed correctly. Thanks! On 07/02/2012 09:41 PM, Greg Von Kuster wrote: > Hello Matthias, > > I've just updated the tool shed