Re: [galaxy-user] Do I need to have tool or dependencies installed in the server to run Galaxy tools?

2012-10-18 Thread Björn Grüning
Hi Sachit, the bismark wrapper is not finished, that's the reason its only in the test-toolshed. When its finished you do not neet bismark to be installed, but bowtie. Cheers, Bjoern I integrated Bismark in Galaxy in my server. I downloaded Bismark from Galaxy Tool shed. I just copied the

Re: [galaxy-user] Error installing MACS on local Galaxy

2012-10-18 Thread Jerzy Dyczkowski
Hi Jennifer, I am now trying to run MACS 1.3.7.1. in Galaxy. I also ran python setup.py install and set variables $PATH and $PYTHONPATH for the commandline run. Nevertheless, MACS gives error: /ImportError: No module named MACS.OptValidator/ I checked - library OptValidator.py exists in the

Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

2012-10-18 Thread Todd Oakley
Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do: ps aux | grep galaxy Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. For example this line: galaxy 11638 0.0

Re: [galaxy-user] Export to file

2012-10-18 Thread Dave Corney
Hi Jeremy, Thanks for your offer of help. By the time I got your email I had already added many new jobs to the history that are either running now or waiting to run. Since I read somewhere that if the history is running then there are problems exporting I shared a clone of the history with you.

Re: [galaxy-user] galaxy MAIN data problem

2012-10-18 Thread Jennifer Jackson
Hello Kshama, We would like to help. I looked for an account under your email address kasw...@masonlive.gmu.edu on the public Main Galaxy instance at http://main.g2.bx.psu.edu (http://usegalaxy.org), and did not find one, so I will tell you how to check for the data yourself, then you can