Installation

Install software

Copy the source files:

git clone https://github.com/ncbi/tree-tool

Remember the directory in the environment variable $TT:

TT=$PWD/tree-tool

Compile all executables in $TT/:

cd $TT
./make.sh 0

The last printed line must be "SUCCESS!".

Update software to a new version

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

Test software

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

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

cd $TT/phylogeny
./distTree_test.sh go
# Time: ~20 min. on a 1200 MHz computer

Create database tables

This is needed for incremental tree building.

Set variables:

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

Create tables:

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

Test bulk insert:

echo -e "5\n10\n15" > list
$TT/database/bulk.sh $SERVER $BULK_LOCAL $BULK_REMOTE list $DATABASE..List
sqsh-ms  -S $SERVER  -D $DATABASE  -m bcp  -C "select id from List"

The result should be:

5|
10|
15|