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ofirrofirr
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dockerization
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‎dockerization/Dockerfile

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#FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:0.1.2
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FROM ubuntu:18.04
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USER root
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RUN apt-get update && apt-get upgrade -y
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RUN apt-get install -y python3.6 vim tmux fish curl wget strace git gcc
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RUN git clone https://github.com/shapirolab/clineage.git
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RUN wget -P /tmp https://repo.anaconda.com/archive/Anaconda3-2021.04-Linux-x86_64.sh
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RUN bash /tmp/Anaconda3-2021.04-Linux-x86_64.sh -b
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ENV PATH /root/anaconda3/bin/:$PATH
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WORKDIR clineage
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RUN mkdir hg19 \
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&& mv get_hg19.bash hg19/ \
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&& cd hg19 \
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&& bash get_hg19.bash
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RUN conda init bash \
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&& . ~/.bashrc \
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&& conda create --name py36 python=3.6 \
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&& conda activate py36 \
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&& conda install -c bioconda -c dranew --file conda_requirements.txt
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RUN echo "click==7.1.2" >> requirements-extra.txt # click version 8 breaks us
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RUN echo "setuptools==57.5" >> requirements-extra.txt # setuptools version 58 breaks us
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RUN . ~/.bashrc && conda activate py36 && pip install -r requirements-extra.txt
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RUN . ~/.bashrc && conda activate py36 && pip install -r requirements.txt
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RUN . ~/.bashrc && conda activate py36 && pip install -r requirements-unpackaged.txt
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RUN tail -n +2 requirements-dev.txt > /tmp/a && mv /tmp/a requirements-dev.txt # Remove redundent line
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RUN . ~/.bashrc && conda activate py36 && pip install -r requirements-dev.txt
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CMD /entrypoint.sh
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#CMD sleep infinity

‎dockerization/build.sh

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#!/bin/bash
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set -euo pipefail
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DOCKER_BUILDKIT=1 docker build -t clineage .

‎dockerization/docker-compose.yml

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version: "3"
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services:
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db:
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image: mariadb
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volumes:
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- db_data:/var/lib/mysql
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restart: always
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environment:
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MYSQL_ROOT_PASSWORD: root_password
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MYSQL_DATABASE: clineage_prod
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MYSQL_USER: dcsoft
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MYSQL_PASSWORD: 164d8ae81bd7e38a163ea2e144114b25
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clineage-web:
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depends_on:
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- db
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image: clineage
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restart: always
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volumes:
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- ./resources/local_settings.py:/clineage/clineage/local_settings.py
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- ./resources/init_once_clineage_web.sh:/init_once.sh
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- ./resources/entrypoint_clineage_web.sh:/entrypoint.sh
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- data_store:/data_store
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ports:
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- 8000:8000
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environment:
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MYSQL_HOST: db
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MYSQL_PORT: 3306
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MYSQL_DATABASE: clineage_prod
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MYSQL_USER: dcsoft
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MYSQL_PASSWORD: 164d8ae81bd7e38a163ea2e144114b25
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task-scheduler:
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image: clineage
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volumes:
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- ./resources/entrypoint_task_scheduler.sh:/entrypoint.sh
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ports:
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- 8787:8787
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restart: always
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clineage-worker:
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depends_on:
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- clineage-web
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- task-scheduler
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image: clineage
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restart: always
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volumes:
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- ./resources/local_settings.py:/clineage/clineage/local_settings.py
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- data_store:/data_store
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# - ./resources/entrypoint_clineage_worker.sh:/entrypoint.sh
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- ./resources/entrypoint_debug.sh:/entrypoint.sh
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environment:
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MYSQL_HOST: db
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MYSQL_PORT: 3306
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MYSQL_DATABASE: clineage_prod
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MYSQL_USER: dcsoft
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MYSQL_PASSWORD: 164d8ae81bd7e38a163ea2e144114b25
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volumes:
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db_data: {}
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data_store: {}

‎dockerization/resources/entrypoint_clineage_web.sh

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#!/bin/bash
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set -e
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bash /init_once.sh
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. $(which activate) py36
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cd /clineage
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./manage.py runserver 0.0.0.0:8000

‎dockerization/resources/entrypoint_clineage_worker.sh

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#!/bin/bash
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set -e
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. $(which activate) py36
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PYTHONPATH='/clineage' DJANGO_SETTINGS_MODULE='clineage.settings' dask-worker --nthreads 1 --memory-limit 300000000000 --preload /clineage/worker-setup.py task-scheduler:8786

‎dockerization/resources/entrypoint_debug.sh

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#!/bin/bash
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set -e
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sleep infinity

‎dockerization/resources/entrypoint_task_scheduler.sh

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#!/bin/bash
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set -e
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. $(which activate) py36
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dask-scheduler

‎dockerization/resources/init_once_clineage_web.sh

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#!/bin/bash
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set -e
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if [ -f /init_done ]; then
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exit
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fi
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. $(which activate) py36
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cd /clineage
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yes "yes" | ./manage.py migrate
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cat <<EOF | python manage.py shell
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from django.contrib.auth import get_user_model
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User = get_user_model() # get the currently active user model,
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User.objects.filter(username='root').exists() or \
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User.objects.create_superuser('root', 'root@example.com', 'root')
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EOF
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touch /init_done

‎dockerization/resources/local_settings.py

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import os.path
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import os
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#CHROMOSOMES_PATH = '/net/mraid11/export/dcstor/Ofir/GenomesData/'
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CHROMOSOMES_PATH = '/clineage/hg19/'
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DEBUG=True
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# S_MAIN = '/net/mraid11/export/dcstor/LINEAGE/Hiseq/NSR2/fastq_human/Output'
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S_MAIN = '/data_store'
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# DATABASES = {
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# 'default': {
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# 'ENGINE': 'django.db.backends.mysql', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
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# 'NAME': 'clineage_prod', # Or path to database file if using sqlite3.
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# 'USER': 'dcsoft', # Not used with sqlite3.
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# 'PASSWORD': '164d8ae81bd7e38a163ea2e144114b25', # Not used with sqlite3.
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# 'HOST': 'db', # Set to empty string for localhost. Not used with sqlite3.
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# 'PORT': '3306', # Set to empty string for default. Not used with sqlite3.
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# }
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# }
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DATABASES = {
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'default': {
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'ENGINE': 'django.db.backends.mysql', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
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'HOST': os.environ['MYSQL_HOST'], # Set to empty string for localhost. Not used with sqlite3.
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'PORT': os.environ['MYSQL_PORT'], # Set to empty string for default. Not used with sqlite3.
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'NAME': os.environ['MYSQL_DATABASE'], # Or path to database file if using sqlite3.
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'USER': os.environ['MYSQL_USER'], # Not used with sqlite3.
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'PASSWORD': os.environ['MYSQL_PASSWORD'], # Not used with sqlite3.
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}
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}
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ALLOWED_HOSTS = [
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'*',
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]
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SECRET_KEY = 'gcd6^pq#l78%_jg3@2jf)csum=_d%5-pa5!3hma4g&e*lxx+m$'
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DATA_STORE = '/data_store'
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# NOA_MATLAB = r'/home/dcsoft/s/Ofir/noa_matlab/Code/'
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NOA_MATLAB = r''
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# IGORS_CODE = r'/home/dcsoft/s/Ofir/igor_tree_reconstruction_20170808/'

‎dockerization/run.sh

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#!/bin/bash
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set -euo pipefail
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docker run --rm -u root --entrypoint /usr/bin/fish -it clineage

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