Prev Next ihme_db.sh

@(@\newcommand{\B}[1]{ {\bf #1} } \newcommand{\R}[1]{ {\rm #1} } \newcommand{\W}[1]{ \; #1 \; }@)@This is dismod_at-20221105 documentation: Here is a link to its current documentation .
Make a Local Copy an IHME Dismod_at Database

Syntax
Purpose
Download
python3
absolute_dir
--user
relative_dir
database
db2csv

Syntax
bin/ihme_db.sh [--user] relative_dir database
Purpose
This script copies a dismod_at database to a local directory and then runs the db2csv_command on the database. This script is only intended to be used by members of IHME and to be run from the IHME cluster. It can also be run on a computer that has mounted the /ihme/epi and /ihme/homes directories.

Download
You must first change into a directory where you have write permission, download dismod_at.git , and then change into the dismod_at.git directory. This script can only be run from the download directory dismod_at.git.

python3
You must inform dismod_at where the python3 executable is located. The setting for this is in the run_cmake.sh file. If that setting is not correct, change it, and then execute the command
 bin/run_cmake.sh
absolute_dir
We use absolute_dir to refer to an absolute path to a directory below which the database is stored before executing this script. You must have read permission below this directory (but do not need write permission). The default value for this directory is
     absolute_dir=/ihme/epi/at_cascade
--user
The brackets around --user indicate that this command line argument is optional. If it is present, absolute_dir is the home directory for the specified user; i.e.,
     absolute_dir=/ihme/homes/user
relative_dir
The command line argument relative_dir is the directory, relative to the absolute directory, where the database is stored before executing this script.

database
The command line argument database is the local name of the database file; i.e., there are no / characters in database . The original database is stored in the location
     absolute_dir/relative_dir/database
db2csv
The original database is copied to the directory
     ihme_db/relative_dir
 relative to the download directory dismod_at.git. We refer to this as the local directory. The db2csv_command is run on the database. The resulting CSV files are all in the local directory.
Input File: bin/ihme_db.sh