Difference between revisions of "Blast2go: b2g4pipe"
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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 | ||
| + | |||
| + | or | ||
| + | |||
| + | Dbacces.dbname=b2g | ||
| + | Dbacces.dbhost=localhost | ||
| + | |||
| + | ==databases == | ||
| + | These are what is required: | ||
| + | |||
| + | * http://archive.geneontology.org/latest-lite/go_20160130-assocdb-data.gz ('''234M''') (this is actually a mysql dump) | ||
| + | * 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''') | ||
Latest revision as of 14:20, 8 February 2016
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.
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
or
Dbacces.dbname=b2g Dbacces.dbhost=localhost
databases
These are what is required:
- http://archive.geneontology.org/latest-lite/go_20160130-assocdb-data.gz (234M) (this is actually a mysql dump)
- 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)
