Commit 0e0a6374 authored by Bryan  BRANCOTTE's avatar Bryan BRANCOTTE
Browse files

Merge branch 'master' into dev

parents baf1f344 7b88d5c5
......@@ -94,8 +94,14 @@ deploy-webserver:
- yum install -y gcc
- yum install -y https://repo.ius.io/ius-release-el7.rpm
- yum update -y
- yum install -y python35u python35u-libs python35u-devel python35u-pip openssl-devel libffi-devel
- pip3.5 install ansible
- yum install -y python36u python36u-libs python36u-devel python36u-pip openssl-devel libffi-devel
- python3.6 -m pip install --upgrade pip
- export PYTHONIOENCODING=utf8
- export LANG=en_US.UTF-8
- export LANGUAGE=en_US:en
- export LC_ALL=en_US.UTF-8
- python3.6 -m pip install ansible
- python3.6 -m pip install virtualenv
- cd ansible
- whoami
- ansible-playbook -vvv -i ./hosts_deploy deploy.yaml --extra-vars "@params-server.json"
......
......@@ -61,6 +61,12 @@
- name: nginx
become: true
yum: name=nginx state=latest
- name: zlib-devel # required by Pillow
become: true
yum: name=zlib-devel state=latest
- name: libjpeg-turbo-devel # required by Pillow
become: true
yum: name=libjpeg-turbo-devel state=latest
- pip:
name: wheel
executable: pip3.6
......
......@@ -19,6 +19,20 @@ We advise users to install jass in a virtual environment
Installation with conda
-----------------------
Installation with pip (recommended)
-----------------------------------
We advise users to install jass in a virtual environment
.. code-block:: shell
python3 -m venv $PATH_NEW_ENVIRONMENT
source $PATH_NEW_ENVIRONMENT/bin/activate
pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/jass.git
pip3 install -r https://gitlab.pasteur.fr/statistical-genetics/jass/-/raw/master/requirements.txt
Installation with conda
-----------------------
A procedure for the correct installation of JASS in Anaconda environment for development purpose is developed in detail below.
**1. Create a specific directory and load the code on your laptop (only the first time)**
......
......@@ -180,17 +180,15 @@ def w_clean_project_data(args):
def w_create_inittable(args):
input_data_path = absolute_path_of_the_file(args.input_data_path)
init_covariance_path = args.init_covariance_path
init_genetic_covariance_path = args.init_genetic_covariance_path
#if genetic and H0 covariance provided search its absolute path
if args.init_covariance_path:
init_covariance_path = absolute_path_of_the_file(args.init_covariance_path)
else:
init_covariance_path = args.init_covariance_path
if init_covariance_path is not None:
init_covariance_path = absolute_path_of_the_file(init_covariance_path)
if args.init_genetic_covariance_path:
init_genetic_covariance_path = absolute_path_of_the_file(args.init_genetic_covariance_path)
else:
init_genetic_covariance_path = args.init_genetic_covariance_path
if init_genetic_covariance_path is not None:
init_genetic_covariance_path = absolute_path_of_the_file(init_genetic_covariance_path)
regions_map_path = absolute_path_of_the_file(args.regions_map_path)
description_file_path = absolute_path_of_the_file(args.description_file_path)
......@@ -391,6 +389,7 @@ def get_parser():
)
parser_create_it.add_argument(
"--init-genetic-covariance-path",
required=False,
default=None,
help="path to the genetic covariance file to import. Used only for display on Jass web application",
)
......
......@@ -7,7 +7,7 @@ import pkg_resources
from setuptools import setup, find_packages
NAME = "jass"
VERSION = "2.1"
VERSION = "2.2"
SETUP_DIR = os.path.dirname(__file__)
README = os.path.join(SETUP_DIR, 'README.md')
......
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