Difference between revisions of "NBIC Galaxy Server: Next Update Requests"

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# [[NBIC_Galaxy_Server:_Maintenance_Guideline#Tools.2Flibraries | Clean and better organize the tool installations]].  
 
# [[NBIC_Galaxy_Server:_Maintenance_Guideline#Tools.2Flibraries | Clean and better organize the tool installations]].  
 
# Customize tool pane and only show pipeline (workflows) and some essential tools. --[[User:Leon|Leon]] 16:38, 9 September 2010 (CEST)
 
# Customize tool pane and only show pipeline (workflows) and some essential tools. --[[User:Leon|Leon]] 16:38, 9 September 2010 (CEST)
# Modify the MySQL database to support UTF-8 unicode. When data sets contain unicode characters not part of the latin-1 encoding in the first few lines of data, the upload of such data sets will fail, because Galaxy tries to store the first few lines of data for the "peek" info.
 
## Stack traces for this symptom will finish with something like this: UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufeff' in position 0: ordinal not in range(256)
 
## This file [[Media:Unicode_test.mzdata]] contains several unicode characters not part of the latin-1 encoding and can be used to check if this issue is resolved.
 
 
# Setting Up the Reference Genomes (Human, Mouse, TAIR?) for NGS Tools (e.g. BWA, Lastz, etc). Refer to http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
 
# Setting Up the Reference Genomes (Human, Mouse, TAIR?) for NGS Tools (e.g. BWA, Lastz, etc). Refer to http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
 
# An automated test on Galaxy after each update
 
# An automated test on Galaxy after each update
 
# A cleanup script to reclaim disk space: check the last access timestamp of history items and delete the ones that were not accessed for 6 ??? months.
 
# A cleanup script to reclaim disk space: check the last access timestamp of history items and delete the ones that were not accessed for 6 ??? months.
# Move Mysql DB to normal location /var/lib/mysql?
 
 
# Backup script?  
 
# Backup script?  
 
# Missing rpy:  
 
# Missing rpy:  

Revision as of 16:03, 3 January 2011

This is a list of update requests on NBIC Galaxy server. They will be discussed prior to the next scheduled update: Monday, 2010-10-04

  1. Clean and better organize the tool installations.
  2. Customize tool pane and only show pipeline (workflows) and some essential tools. --Leon 16:38, 9 September 2010 (CEST)
  3. Setting Up the Reference Genomes (Human, Mouse, TAIR?) for NGS Tools (e.g. BWA, Lastz, etc). Refer to http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
  4. An automated test on Galaxy after each update
  5. A cleanup script to reclaim disk space: check the last access timestamp of history items and delete the ones that were not accessed for 6 ??? months.
  6. Backup script?
  7. Missing rpy:
"An error occurred running this job: Traceback (most recent call last):
File "/nbic/prog/galaxy-2010-11-14/tools/stats/grouping.py", line 7, in
<module>
from rpy import *
ImportError: No module named rpy"