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HistoneDB via virtual machine

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
cd histonedb
git checkout histonedb_py27
cd ../
mkdir db

Then you can run HistoneDB via two ways.

Running via docker

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

docker run --name histdb -d -p 8080:10080 -v project_dir/histonedb:/var/www/histonedb -v project_dir/db:/var/lib/mysql intbio/histonedb:0.0.1

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:0.0.1

  • Run apache on prot 10080 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

  • 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,

For development

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