mmeds-meta

Instructions

In order to run the mmeds server locally you will need.

• Some mysql server running on your machine. For development we are using mariadb.
  To install on linux install the mariadb and mariadb-server packages using your distro’s manager.
  For other OS’s the installer can be found here

• A mongoDB server running on your machine. Installers can be found here

To setup the SQL database connect to you sql database as root:
mysql -u root
Then run the following command.
source setup.sql;

mmeds is written in in Python3 so you will need a python3 environment to run it.
Run python setup.py install to install the necessary dependencies.

To start the server change to the host directory and run python host.py 1

To connect to the server go to MMEDS
Allow access to the webpage despite your browsers warning. The security certificate is not signed.

NOTE: Certain versions of openssl as installed by conda cause issues with cherrypy ssl.
To fix this run conda install openssl=1.0.2p. This version should work.

The directory that uploads are saved in are determined by the value of
the MMEDS environment variable. If this variable is not set it defaults
to the current user’s home directory.

Latex Dependencies
adjustbox
upquote
ulem
revtex
braket

Other Dependencies
rpy2: 2.9.1
readline headers
jupyter_contrib_nbextensions

latex_template

font

If you encounter INVALID DISPLAY VARIABLE add the line backend: agg to your matplotlibrc
(typically ~/.config/matplotlib/matploblibrc)
or setup your environment with export MPLBACKEND="agg"

To install Qiime1.9.1 with a recent version of conda run:
conda config --set allow_conda_downgrades true
conda install conda=4.6.14
Prior to running the conda command for installing Qiime