histonedb

HistoneDB via virtual machine

TL;DR; for Docker in OSX

mkdir project_dir
cd project_dir
git clone https://github.com/intbio/histonedb.git
mkdir db
cd ..
docker stop histdb; docker rm histdb # optional if container exists and is running
docker run --name histdb -d -p 8080:10081 -v `pwd`/project_dir/histonedb:/var/www/histonedb -v `pwd`/project_dir/db:/var/lib/mysql intbio/histonedb:0.2.1
docker exec -it histdb bash -c "bash /var/www/db_gen.sh -mysql_db_reinit -histdb_reinit"

Check the website at http://localhost:8080

Instructions

Prepare directories and clone repo

Create project directory and directories where to mount project code and database

mkdir project_dir
cd project_dir
git clone https://github.com/intbio/histonedb.git
mkdir db
cd ..

Then you can run HistoneDB via two ways.

Running via docker (allow at least 4Gb of RAM + 4 Gb of SWAP in Docker preferences)

• Run as a service in docker, this will run apache and attempt to start mysqld

  docker stop histdb; docker rm histdb # optional if container exists and is running
  docker run --name histdb -d -p 8080:10081 -v `pwd`/project_dir/histonedb:/var/www/histonedb -v `pwd`/project_dir/db:/var/lib/mysql intbio/histonedb:0.2.1
  

• Check the website is available at http://localhost:8080

• Get into container and start db regeneration

docker exec -it histdb bash

• Next in reinit_histdb_local.sh adjust the database you would want to build HistoneDB from (swissprot, nr, etc.)

bash db_gen.sh -mysql_db_reinit -histdb_reinit

• To stop the container run

docker stop histdb

Run in singularity

• Build singularity container

singularity build --sandbox cont docker://intbio/histonedb:0.2.1

• Run apache on prot 10081 and attempt to start mysqld

singularity instance start --writable --bind project_dir/histonedb:/var/www/histonedb,project_dir/db:/var/lib/mysql cont histdb

• Get into container

singularity shell instance://histdb

• Regenerate db

apachectl start
cd /var/www

• Next in reinit_histdb_local.sh adjust the database you would want to build HistoneDB from (swissprot, nr, etc.)

bash db_gen.sh -mysql_db_reinit -histdb_reinit or bash db_gen.sh -mysql_db_reinit -histdb_reinit > histonedb/log/db_gen.log 2>histonedb/log/db_gen_error.log

• To stop the container run

singularity instance stop histdb

**IMPORTANT NOTE: Looks like singularity is not completele isolated from the host machine kernel security modules, e.g. apparmor. So it means on the host /etc/apparmor.d/usr.sbin.mysqld should have

# Allow data files dir access
  /var/lib/mysql-files/ r,
  /var/lib/mysql-files/** rwk,

Run a second indtance in singularity

Use singularity build --sandbox cont docker://intbio/histonedb:0.2.0p2 And change port to port = 13307 in HistoneDB/database_info.txt The running port of web server willbe 10081

For development

• Profiling python -m cProfile -s cumtime manage.py buildvariants

• Imaging

  docker image build -t intbio/histonedb:0.2.0 .
  docker push intbio/histonedb:0.2.0