SERVER_SETUP.md

HistoneDB setup instructions

HistoneDB can be run simple from file run.sh. This script contains some steps:

1. Install full list of server dependencies by the script system_setup/full_setup.sh. See requirements.

2. Apache2 and WSGI configuration. More info described in configuration instructions.

3. Database creation (see database configurations).

4. Project setup.

Project setup

Starting the project include following steps.

1. Storing the login information in the file HistoneDB/NCBI_databse_info.txt, which is formatted in the following way (key = value):

name = DB_NAME
user = DB_USER
password = DB_PASS
host = DB_HOST
port = DB_PORT
SECRET_KEY = DJANGO_SECRET_KEY

#Reference another file with same paramters, useful if it needs be hidden
file = /path/to/other/file.txt

#Root of site when accessed from a browser
STATIC_URL = /static/ 

2. Migrations of Django models into database:

python manage.py migrate

3. Building NCBI Taxonomy with djangophylocore:

python manage.py buildncbi
python manage.py loadtaxonomy
python manage.py buildtaxonomytoc

WARNING: This will download the entire NCBI taxonomy database and load into the database, which can take a long time.

4. Classification of sequences in NR:

python manage.py buildvariants

WARNING: This will by default download the entire nr database and classify all sequences in the nr. If you want to build the HistoneDB using a smaller database of proteins in FASTA format using the NR formatted header (">UNIQUE_ACCESSION|anything description [TAXONOMY_NAME]"), run the following command:

python manage.py buildvariants --db small_database.fasta

5. Building trees from seed sequences:

python manage.py buildtrees

6. Building organism sunbursts for each variant:

python manage.py buildsunburst

7. Building Blast database for custom sequence analysis:

python manage.py buildblastdb

8. Building variantinfo:

python manage.py buildvariantinfo

9. Building GFF sequence features for variants:

python manage.py buildseedinfo

Update

If youe need to update or rebuild the database, e.g. if a new variant is discovered, you must rerun steps 4-8 adding the --force parameter after each command to make sure everything gets updated.

Adding new variants

1. Collect representative sequences of the new variant and create seed alignments using any method you wish. Please read our paper for more info on how we collected the sequences and aligned them.

2. Place seed alignments in appropriate static directory:

static/browse/seeds/[HISTONE_TYPE]/[VARIANT].fasta

3. Follow update instructions

4. If this is a new variant, please let us know by creating a pull request, a new issue (enhancement), or emailing us.