Commit d31f357b authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

update docs

parent 3b553150
......@@ -10,7 +10,7 @@ Linux installation
This package contains patches for **CNS-solve** which needs to be compiled
with the sources after the installation. Please follow post installation
instruction before using ``aria2`` pipeline.
instruction before using `aria2` pipeline.
Dependencies
------------
......@@ -19,8 +19,6 @@ Before starting the installation procedure, be sure to check if dependencies
below are actually correctly installed in your environment.
* **pip** (>= 9.0)
* **setuptools** (>= 18.0)
* **numpy**`` (>= 1.11)
* **cns-solve** (1.21)
* **ccpnmr analysis** (optional)
* **ccpn data model** (optional)
......@@ -29,26 +27,16 @@ CNS-solve
+++++++++
The only piece of Fortran code that needs to be compiled together with your
CNS sources can be found in ./cns/src; only the code for floating
chirality assignment is being used. The installation procedure has not
changed since ARIA version 1.2:
CNS sources can be found in `src/aria/cns/src`> Only the code for floating
chirality assignment is being used. The procedure has not changed since ARIA version 1.2:
a) Academic users can obtain a free version of CNS from the CNS web site:
a. Academic users can obtain a free version of CNS from the [CNS web site](http://cns.csb.yale.edu). Commercial users need to purchase a CNX license from Accelrys (MSI).
http://cns.csb.yale.edu
b. The ARIA fortran sources are located in the subdirectory `./cns/src` of the distribution. Please copy all the files to the directory cns_solve_1.1/source of the unpacked cns_solve distribution (this will overwrite some files which is okay).
Commercial users need to purchase a CNX license from Accelrys (MSI).
c. Edit the file "cns_solve_env" in the directory cns_solve_1.1 to define the location of the CNSsolve directory.
b) The ARIA fortran sources are located in the subdirectory ./cns/src of
the distribution. Please copy all the files to the directory
cns_solve_1.1/source of the unpacked cns_solve distribution (this will
overwrite some files which is okay).
c) Edit the file "cns_solve_env" in the directory cns_solve_1.1 to define the
location of the CNSsolve directory.
d) Go to directory cns_solve_1.1 and type "make install". This should start
the compilation process.
d. Go directory to cns_solve_1.1 and type "make install". This should start the compilation process.
CCPNMR
......@@ -59,28 +47,50 @@ also need to install the CCPN data model, and the CCPNMR Analysis software in
case you want to export restraint lists, NOE assignments, and analyses of the
generated structures, e.g. the result of the violation analysis. The complete
CCPN distribution including the API, the FormatConverter, and CCPNMR Analysis
can be obtained :ref:`here <http://www.ccpn.ac.uk/ccpn/software/downloads-v2/>`_
can be obtained [here](http://www.ccpn.ac.uk/ccpn/software/downloads-v2/).
The CCPN distribution provides scripts which guide you through the
installation process.
Using pip
---------
Using virtualenv & pip
----------------------
The recommended installation process is to install the package with [pip inside a virtual environment](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/).
.. warning::
The recommended installation process is to use an up to date ``pip`` command with
the last ``ariaec`` version. For the moment, the packages used Python 2.7 but
the transition to Python 3 is planned in the near future.
For the moment, the package use *Python 2.7* but the transition to Python 3 is
planned in the near future.
To install the latest stable release, do the following steps on your terminal :
1. Install or update `pip` and `virtualenv` in your current python environment
.. code-block:: shell
python -m pip install --user --upgrade pip virtualenv
2. Go to your project directory and create a virtual environment by giving the name of
a directory to place the new virtual environment (e.g. `venv`).
.. code-block:: shell
python -m virtualenv venv
3. Activate the new environment and install the latest release from GitLab.
.. code-block:: shell
Then the easiest solution is to call the command below :
source venv/bin/activate
pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
From source
-----------
Even though it is not recommanded, another possibility is to download the ZIP_
Even though it is not recommended, another possibility is to download the ZIP_
or TAR_ version from Gitlab_, extract the files and run ``pip`` inside the new
directory.
......
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