Introns database builder

Installation

Requires Qt version 4.x or 5.x with MYSQL support. Check your installation.

qmake
make
make install

**Note 1: ** in some distros you should type qmake-qt4 or qmake-qt5 corresponding to Qt's version to use instead of qmake command.

**Note 2: ** default installation location is /usr/local/bin. You can override the path by passing PREFIX=somewhere after qmake command.

Usage

Common usage

introns_db_fill [OPTIONS] FILENAMES

• FILENAMES - a list of GBK of compressed GBK (*.gbk.gz) file names to be processed. It is possible to pass a wildcard instead of list, e.g. *.gbk.gz or something like this
• OPTIONS - optional additional parameters

Additional parametets

Database connections parameters:

• --host=HOST_NAME - use HOST_NAME to connect MySQL. If not provided, then localhost will be used
• --user=USER_NAME - use USER_NAME to connect MySQL. If not provided, then root will be used
• --pass=PASSWORD - the password for user. Default is empty
• --db - MySQL database name. Default is introns

Input parameters:

• --use-data=DATAFILE.ini - use additional data from DATAFILE.ini. If not specified, then correspoding by name .ini file will be used for each GBK input, if exists

Output parameters:

• --seqdir=OUTPUT_DIR_NAME - store origins into OUT_DIR_NAME direcory. If not specified, then origins will not be stored.

Processing parameters:

• --threads=NUM_THREADS - use specified NUM_THREADS workers to process. By default, all processors/cores will be used