hendersonmpa/porph-screen

porphyrin screening app

Porphyrin Screen Interpretation

Setup

• $ indicates the shell prompt
• * indicates the sbcl prompt

Overview

1. Install SBCL Common Lisp
2. Istall rlwrap - makes it easier to work at the sbcl command prompt
3. Install Quicklisp - the package manager
4. Install Sqlite3
5. Install Gnuplot for graphs
6. Create directories
7. Clone the porph-screen repo from github

Install SBCL

• Install SBCL from source to get the latest version
• First install an old version of SBCL
  • SBCL needs a lisp to compile itself therefore
  • $ sudo apt install sbcl
• Download SBCL source code from http://www.sbcl.org/platform-table.html
• Extract it (version numbers will change)
  • $ bzip2 -cd sbcl-2.x.x-source.tar.bz2 | tar xvf -
  • $ cd sbcl-2.x.x
  • $ sh make.sh –dynamic-space-size=60Gb –fancy
• Optional tests and documentation
  • $ cd tests && sh ./run-tests.sh
  • $ cd ../doc/manual/ && make
  • $ cd ../.. ## back to sbcl-2.x.x
  • $ sudo sh install.sh

Install rlwrap

• $ sudo apt install rlwrap
• Add the following line to .bashrc
  • alias sbcl=’rlwrap /usr/local/bin/sbcl’

Install Quicklisp

https://www.quicklisp.org/beta/

• Download the script to a suitable directory
  • $ curl -O http://beta.quicklisp.org/quicklisp.lisp
• Load this file in sbcl
  • $ sbcl –load quicklisp.lisp
• Start sbcl as follows:
  • $ sbcl
• Run the following at the sbcl prompt “*”
  • * (quicklisp-quickstart:install)
  • * (ql:add-to-init-file)

Install sqlite3

• db engine and libraries
  • $ sudo apt install sqlite3 libsqlite3-dev

Install gnuplot

• $ sudo apt install gnuplot

Clone repositiory

• Make the following directory
  • $ sudo mkdir ~/common-lisp
• Navigate to ~/common-lisp
  • $ git clone
  • $ cd ~/common-lisp
  • $ git clone https://github.com/hendersonmpa/porph-screen.git

Test

• Navigate to ~/common-lisp/porph-screen
  • $ sbcl –load “start-app.lisp”
• It will confirm or create a data directory and a db file
  • ~/data/
  • ~/data/porph_screen.sqlite
• In a browser navigate to
  • localhost:4242/select
• End the process either by closing the terminal or Ctrl-C and selecting EXIT

Run in the background

• Navigate to ~/common-lisp/porph-screen
• $ ./start-app.sh
• This script runs the app in a detached screen session.
• To reattach
  • $ screen -r
• The process can be ended closing the terminal or Ctrl-C and selecting EXIT