Differences

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--- chado [2010/01/14 09:17]
172.26.15.184
+++ chado [2010/05/22 14:19]
@@ Line 1: / Line 1: @@
-====== Chado ======
-Create new T.pava Chr1 Chado database from Chr1 Genbank file. Local version of Genbank file does not work. Downloaded new file from Genbank: NC_001142.gbk
-Convert file to gff using script:
-<code>genbank2gff3.pl</code>
-Create pgsql database.
-<code>createdb --template=chado tparvadb
-psql tparvadb
-chado> SELECT * FROM organism;
-chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');
-chado> \q</code>
-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>
-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>

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