[galaxy-user] tool_type="data_source_async"

2012-01-03 Thread Matt Vincent
Hello all, I am trying to configure an Asynchronous tool (I can get it to work synchronously). My configuration looks something like this for the tool: mytool description data_source.py $output $__app__.config.output_size_limit http://myurl"; check_values="false" meth

Re: [galaxy-user] Not able to get data from UCSC table browser

2012-01-03 Thread Nate Coraor
On Dec 22, 2011, at 5:35 PM, Sell, Christian wrote: > Hi, > > I encountered similar problems today. I can’t open some histories, upload > data or transfer data between histories. > > Regards > > Christian Hi, Due to extremely high load at the time, jobs were delayed. This has been resol

Re: [galaxy-user] problem upload data file

2012-01-03 Thread Nate Coraor
On Dec 28, 2011, at 10:36 AM, Eric Guo wrote: > Hi everyone, > > I'd like to upload my sequencing data file, 36 GB, onto galaxy. My data is on > a computer cluster in my institute. So I use ssh shell ftp commands to > connect to galaxy and upload the data(ftp> put filename). And the connection

Re: [galaxy-user] ftp upload

2012-01-03 Thread Nate Coraor
On Dec 27, 2011, at 8:52 PM, Gabor Bartha wrote: > I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs > have been failing with: > 421 service not available, remote server has closed connection > after about 1.5GB. > > Isn’t ftp the way you are supposed to upload large fi

[galaxy-user] Problem with XML tag

2012-01-03 Thread Greg Edwards
Hi, I'm in the process of adding a proteomics Perl script into a local copy of Galaxy. It seems like the version command in the galaxy/tools/myTools/myPerlTool.xml needs to have a full pathname. The doco indicates this should be enough: myPerlTool -version, and the few examples of it's use in g

[galaxy-user] Config info for: Problem with XML tag

2012-01-03 Thread Greg Edwards
Sorry folks, forgot the basics. It's a fresh install on Mac OS X 10.6.8 Started with sh run.sh in /Users/me/bio/galaxy Everything default. hg heads: changeset: 6298:b258de1e6cea tag: tip user:jeremy goecks date:Thu Nov 17 15:08:49 2011 -0500 summary: Pack js sc

Re: [galaxy-user] Problem with XML tag

2012-01-03 Thread Peter Cock
On Tuesday, January 3, 2012, Greg Edwards wrote: > Hi, > I'm in the process of adding a proteomics Perl script into a local copy of Galaxy. > It seems like the version command in the galaxy/tools/myTools/myPerlTool.xml needs to have a full pathname. > The doco indicates this should be enough: myP