Differences

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--- chado [2010/01/13 09:07] – 172.26.15.184
+++ chado [2010/05/22 14:19] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Chado ======
-createdb --template=chado tparvadb
+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
-psql chado
+Convert file to gff using script:
- chado> SELECT * FROM organism;
+<code> bp_genbank2gff3.pl NC_001142.gbk</code>
- chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');
- chado> \q
+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.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>