README.md

xiView_container

brings together various git project from Rappsilber Laboratory to provide a search software independent web interface to CLMS data. It uses the git submodule mechanism (except for xiAnnotator at the moment).

Installation Instructions

1. Checkout out this github project, initialising submodules

git clone --recurse-submodules https://github.com/Rappsilber-Laboratory/xiView_container.git

2. Install Apache, PostgreSQL, PHP postgres modules

3. Initialise the database by running the schema.sql script from this project

you will need to search and replace on the schrema.sql to swap 'username' for your PostgreSQL user name

4. Configure the python environment for the file parser

Follow the instructions at https://github.com/Rappsilber-Laboratory/xiSPEC_ms_parser but you don't need to install sqlite; instead you need to edit the file xiSPEC_ms_parser/credentials.py to point to your postgress database.

5. Install xiAnnotator

Follow the instructions at https://github.com/Rappsilber-Laboratory/xiAnnotator/tree/master/doc/SysV

6. Edit yet more config files (todo - tidy this up)

Edit ./connectionString.php so it points to your PostgreSQL database Edit ./xiSPEC_config so it points to your xiAnnotator service

.gitignore will ignore your changes to these files

Copy the xi_ini directory in this project into the project parent directory cp ./xi_ini ../xi_ini Edit ../xi_ini/emailInfo.php to contain the information needed for user registration, this is (i) your google recaptcha secret key, and (ii) the email account details. The email account is used to send confirmation emails and password reset requests.