[galaxy-dev] macs error

Hi, I also have problems with macs and macs2 after update. I got this error which seems a python version issue. But I can not find this file. File cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py, line 82, in respond ImportError: No module named simplejson Any suggestions?

Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)

Hi Greg, I figured it out. I forgot to check the box Check to uninstall or leave blank to deactivate . I need to uninstall the tool shed but I leave the box blank firstly. So, it is not uninstalled but just deactivated. Thank you so much! From: Greg Von Kuster

[galaxy-dev] Unable to remove old datasets

Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets 1. delete_userless_histories.sh 2. purge_histories.sh 3.

Re: [galaxy-dev] Unable to remove old datasets

Have the owners of the old datasets marked them as permanently deleted? Peter On Thu, Mar 13, 2014 at 5:35 PM, Sanka, Ravi rsa...@jcvi.org wrote: Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in:

[galaxy-dev] Empty history pane

Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I

[galaxy-dev] Write permission for database/files

Hi All, Galaxy opens a directory under database/files when the #of data files increased. So, it goes 1,2,3 … etc. I want to give a write permission for these specific directories when they are created without changing umask in the user profile. Is there anybody who can tell me where galaxy

[galaxy-dev] installed bwa but there are no bwa files produced in galaxy-dist folder

Hello guys, I've got a problem with the integration of the BWA Tool in Galaxy. I installed BWA and Galaxy in a virtual box and now I want integrate BWA as a tool. For this I have to do this steps: $ sudo cp /home/ubuntu/galaxy-dist/bwa-0.7.4/bwa /usr/local/bin now bwa can be run from the

Re: [galaxy-dev] Puppet Modules

Hi Eric and Sys Admin, It's a great news ! We have already published a puppet module for a basic galaxy install and update: http://forge.puppetlabs.com/urgi/galaxy We also plan to update it for configuration files management. Eric, it could be a great initiative to merge our efforts in a

[galaxy-dev] Purging datasets as part of workflow?

Hi, Is there an automatic way to permanently delete and purge datasets that are the result of intermittent tools in a workflow? That is, how can one automatically keep only the first and the last steps of an workflow without having to manually delete all the intermittent datasets and running

Re: [galaxy-dev] Purging datasets as part of workflow?

On Thu, Mar 13, 2014 at 6:30 PM, Sveinung Gundersen sveinung.gunder...@medisin.uio.no wrote: Hi, Is there an automatic way to permanently delete and purge datasets that are the result of intermittent tools in a workflow? That is, how can one automatically keep only the first and the last

Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets

I do not think so. Several individual datasets have been deleted (clicked the upper-right X on the history item box) but no History has been permanently deleted. Is there any indication in the database if target dataset or datasets were marked for permanent deletion? In the dataset table, I see

Re: [galaxy-dev] 回复： Re: Local Galaxy web layout

Hello Shenwiyn, the position of the menu items is defined by the order of these items in the galaxy.menu.js file. What do you mean by changing the galaxy interface? Martin On Mon, Mar 10, 2014 at 8:27 AM, Weiyan Shen shenw...@gmail.com wrote: Hi Sam, Using static/scripts/galaxy.menu.js,I

[galaxy-dev] tool_sheds_errors

Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the

Re: [galaxy-dev] tool_sheds_errors

On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to

Re: [galaxy-dev] Empty history pane

If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th