User Tools

Site Tools


chado

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
chado [2010/01/14 08:12] 172.26.15.184chado [2010/05/22 14:19] (current) – external edit 127.0.0.1
Line 4: Line 4:
  
 Convert file to gff using script: Convert file to gff using script:
-<code>genbank2gff3.pl</code>+<code> bp_genbank2gff3.pl NC_001142.gbk</code>
  
 Create pgsql database. Create pgsql database.
Line 17: Line 17:
  
 Load gff3 data into database Load gff3 data into database
-<code>gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gb.gff</code>+<code>gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gbk.gff</code>
  
 +Install Gbrowse2
  
 +<code>**Beginning interactive configuration**
 +Directory for GBrowse's config and support files? [/etc/gbrowse2] 
 +Directory for GBrowse's static images & HTML files? [/var/www/gbrowse2] 
 +Directory for GBrowse's temporary data [/var/tmp/gbrowse2] 
 +Directory for GBrowse's example databases [/var/www/gbrowse2/databases] 
 +Directory for GBrowse's CGI script executables? [/usr/lib/cgi-bin/gb2] 
 +Internet port to run demo web site on (for demo)? [8000] 
 +Apache loadable module directory (for demo)? [/usr/lib/apache2/modules] 
 +User account under which Apache daemon runs? [www-data] 
 +Automatically update Apache config files to run GBrowse? [y] 
 +Automatically update system config files to run gbrowse-slave? [y] 
 +</code>
chado.1263456720.txt.gz · Last modified: 2010/05/22 14:19 (external edit)