Installation

Install software

Create the directory dm/ in the current directory and copy all source files into it.

git clone https://github.com/vbrover/dm.git

Remember the directory in the environment variable $DT:

DT=$PWD/dm

Compile all executables in $DT/:

cd $DT
./make.sh

The last printed line must be "SUCCESS!".

Update software to a new version

cd $DT
git pull origin master
./make.sh

Test software

Slow due to extra checks.
Each test should print "SUCCESS!" at the end.

cd $DT/dm
./dm_test.sh 1
# Time: ~1 min.

cd $DT/phylogeny
./distTree_test.sh go
# Time: ~50 min. on a 1200 MHz computer

Create database tables

This is needed for incremental tree building.

Set variables:

SERVER=...
DATABASE=...
# bulk insert directory
BULK_LOCAL=...
# path in Universal Naming Convention to the bulk insert directory
BULK_REMOTE=...

Then create the tables:

sqsh-ms  -S $SERVER  -D $DATABASE  -i $DT/database/distTree_inc.sql