Blast2go: b2g4pipe - Revision history

Rf: /* Installation and configuration */

2016-02-08T14:20:15Z

‎Installation and configuration

Rf: /* databases */

2016-02-08T14:19:35Z

‎databases

Rf at 14:13, 8 February 2016

2016-02-08T14:13:43Z

Rf at 14:11, 8 February 2016

2016-02-08T14:11:40Z

Rf: Created page with "Blast2go is the gene ontology annotation program for eukaryotes. Some time after 2012, it became commercialised, although the free usage of early version is still permitted...."

2016-02-08T13:58:50Z

Created page with "Blast2go is the gene ontology annotation program for eukaryotes. Some time after 2012, it became commercialised, although the free usage of early version is still permitted...."

New page

Blast2go is the gene ontology annotation program for eukaryotes.

Some time after 2012, it became commercialised, although the free usage of early version is still permitted.

Blast2go the program is GUI, but there is a command-line alternative called b2g4pipe.

The best version of b2g4pipe to use is
http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

As this is the one Peter Cock uses for the Galaxy wrapper version 8 in March 2015.

@@ Line 13: / Line 13: @@
 Aspects required:
- * blast2go.properties file
+* blast2go.properties file
- * databases
+* databases
 ==blast2go.properties==

@@ Line 27: / Line 27: @@
 ==databases ==
-These are what is required.
+These are what is required:
+* http://archive.geneontology.org/latest-lite/go_20160130-assocdb-data.gz ('''234M''') (this is actually a mysql dump)
-* http://archive.geneontology.org/latest-lite/go_20120526-assocdb-data.gz ('''105M'''), se trata de un '''dump''' SQL.
+* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz('''236M''')
 * ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''578M''')
 * ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''2900M''')

@@ Line 21: / Line 21: @@
   Dbacces.dbhost=publicdb.blast2go.com
 ==databases ==
 These are what is required.
-El fichero '''blast2go.properties''' contiene los datos de las BBDD necesarios para '''Blast2go''' en las siguientes líneas:
 * http://archive.geneontology.org/latest-lite/go_20120526-assocdb-data.gz ('''105M'''), se trata de un '''dump''' SQL.
 * ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz('''157M''')
-* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''373M''')
+* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''578M''')
-* ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''900M''')
+* ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''2900M''')

← Older revision		Revision as of 14:11, 8 February 2016
Line 9:		Line 9:

	As this is the one Peter Cock uses for the Galaxy wrapper version 8 in March 2015.		As this is the one Peter Cock uses for the Galaxy wrapper version 8 in March 2015.
		+
		+	=Installation and configuration=
		+
		+	Aspects required:
		+	* blast2go.properties file
		+	* databases
		+
		+	==blast2go.properties==
		+	This is the main configuration file. A normal user can also have a copy in his/her directory , and can try and use it instead. Example:
		+	Dbacces.dbname=b2g_nov11
		+	Dbacces.dbhost=publicdb.blast2go.com
		+
		+
		+	==databases ==
		+	These are what is required.
		+	El fichero '''blast2go.properties''' contiene los datos de las BBDD necesarios para '''Blast2go''' en las siguientes líneas:
		+
		+	* http://archive.geneontology.org/latest-lite/go_20120526-assocdb-data.gz ('''105M'''), se trata de un '''dump''' SQL.
		+	* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz('''157M''')
		+	* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''373M''')
		+	* ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''900M''')
		+
		+
		+	En el caso de nodo '''chubby''', las bases de datos son locales (instaladas anteriormente) que hace que sea mucho más rápida el programa. Por tanto, la ubicación de las BBDD es:
		+	Dbacces.dbname=b2g
		+	Dbacces.dbhost=localhost