[galaxy-dev] Change Manage data Libraries

2012-03-14 Thread Sivasangari NANDY
Hello everyone, I'm trying to change some options in the Manage data Libraries.Especially in the Server Directory, by clicking the Upload directory of file in Upload option. So I've changed universe_wsgi.ini file and add for library_import_dir my directory. The problem is that I can see only

[galaxy-dev] problem after last upgrade

2012-03-14 Thread Michal Stuglik
Dear galaxy, I have upgraded my galaxy-dist with last official version ( upgrade: % hg pull -u -r 40f1816d6857 ). I also upgraded database (sh manage_db.sh upgrade). now I have problem with running galaxy instance and this is what I get:

[galaxy-dev] Exporting worflow to local instal

2012-03-14 Thread Muehlschlegel, Jochen D.,M.D.
Hi, I would like to download/export my workflows from the Galaxy main to a local install at my institution. When I use the URL method, I get the following error message: Data at 'http://main.g2.bx.psu.edu/u/muehlsch12/w/imported-tophat---cuffdiff-paired-end-fastq ' does not appear to be a

Re: [galaxy-dev] Error starting Galaxy after update of March 2012

2012-03-14 Thread Alban Lermine
Nate Coraor wrote: On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote: Hi Alban, Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ? What happens if you run `python scripts/fetch_eggs.py` by hand? Is there

Re: [galaxy-dev] Authentic problem about uploading files to GenomeSpace

2012-03-14 Thread Daniel Blankenberg
Hi Hanfei, I would strongly suggest against having an input field for a password in a Tool, it is not secure at all. Also, as an FYI, we're working locally on GenomeSpace interoperability functionality and it should be released relatively soon, so you may want to hold off on your efforts for

Re: [galaxy-dev] Change Manage data Libraries

2012-03-14 Thread Carlos Borroto
On Wed, Mar 14, 2012 at 6:07 AM, Sivasangari NANDY nsi...@hotmail.com wrote: I've tried to write two times library_import_dir but it's not working, only the last directory is taken into account :                   library_import_dir = /sequences/fasta/maize/                  

Re: [galaxy-dev] [galaxy-user] How to Pass Parameter

2012-03-14 Thread Carlos Borroto
On Tue, Mar 13, 2012 at 2:15 PM, La Chi the_man.in...@yahoo.com wrote: hi galaxy developers , i have developed this parameter in xml file and i am passing  tl value to a function which is present in my python file , but when i select its type=text , it shows a text field with  tl , all i want

Re: [galaxy-dev] Galaxy: enable uploading via FTP

2012-03-14 Thread Nate Coraor
On Mar 12, 2012, at 5:15 PM, jiechenable1...@gmail.com wrote: Dear Nate, Sorry to trouble you. I know that you are busy, but this problem has annoyed me for couple days. Please help. I want to enable uploading via ftp for my local Galaxy instance. I followed the instructions under the

Re: [galaxy-dev] Galaxy server configuration question

2012-03-14 Thread Nate Coraor
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote: Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot /var/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website

Re: [galaxy-dev] Error while uploading

2012-03-14 Thread Nate Coraor
On Mar 12, 2012, at 2:23 PM, Fields, Christopher J wrote: You can change the default location of tmp files by modifying the environment; we ran into this with samtools directly dumping temp sort files to a local node, causing the job to shut down. Setting TMPDIR worked for me. Hi Chris,