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Bart Hazes — Sun, 28 Jul 2013 20:54:19 -0000

For local installation follow the following steps

1) Install mongodb
For more information about mongodb go to its home page http://www.mongodb.org/
Here you can find documention and download mongodb binaries for many platforms including Windows, Mac Os X, Solaris, and Linux
For Ubuntu you can also use the 10gen repository as follows:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10

echo 'deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen' | sudo tee /etc/apt/sources.list.d/10gen.list

sudo apt-get update

sudo apt-get install mongodb-10gen

Optionally: change the vi /etc/mongodb.conf configuration file as needed.

On the command line type: mongo
This connects to the daemon and establishes an interactive interface
At the prompt type: show dbs
This lists the default database(s). Just "local" in my install.

2) Install the Aspera file transfer software for fast NCBI data downloads. See the NCBI site for installation instructions

3) Create the CDSbank database. Download the following scripts and programs

Scripts
rebuildDB.sh Complete rebuild of all databases
get_taxDB.sh Rebuild of the taxonomy database
updateDB.sh Update of subset of Genbank sections
update.make Called by updateDB.sh to allow parallel updates of files

Programs
Taxonomy2Mongo.py Python program to convert the NCBI taxonomy to a mongo DB
GB2mongo.py Read genbank files and load each entry into mongo DB

Libraries
GBmongo.py Main python library for CDSbank programs
genbank.py Python library to parse genbank files
seqlib.py Python library with basic sequence handling routines
geneticCode Python library with genetic code handling routines

The scripts use environment variable CDSBANK, which should be set to the directory with scripts. Programs and libraries should be installed in directories where they will be found automatically or PATH and/or PYTHONPATH should be set appropriately.

For the first build or full rebuild issue the command
./rebuild.sh 196
where 196 is the current Genbank release number
This will first build the taxonomy database, then all whole-genome shotgun data, refseq, genbank except the CON division, the CON division (CON depends on all other genbank raw DNA sequences being available and must come last).

rebuild.sh will call updateDB.sh but you can use updateDB.sh yourself as well as follows

./updateDB.sh LOCALdirectory NBCIdirectory FILEquery
All genbank files in the NCBIdirectory that contain the string FILEquery will be copied to LOCALdirectory and processed. For example:

updateDB.sh refseq refseq/release/complete [^r].gbff.gz
Processes all non-mstr gbff.gz files from the refseq/release/complete directory of ncbi and places the results in the refseq directory. If the command is repeated only files with a different name or size will be downloaded and processed.

Home modified by Bart Hazes

Bart Hazes — Sun, 28 Jul 2013 17:58:18 -0000

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