stopgap-addons

A set of add-ons for enhancing the STOPGAP experience.

Installation instructions

0. Install dependencies:

• STOPGAP obviously. Please refer to the STOPGAP manual for installation and configuration details.
• MATLAB (which you probably already have since you are running STOPGAP)
• IMOD
• gnuplot (possibly already available in your Linux system or HPC environment)
• There is one script (sgstar2bild) that relies on pyem being available

1. Clone this repo:

git clone https://github.com/CellArchLab/stopgap-addons.git

2. Configure environment variables as follows (for example, in your ~/.bashrc file):

export STOPGAP_ADDONS_HOME=/path/to/stopgap-addons/
export PATH=${STOPGAP_ADDONS_HOME}/bash:$PATH
export PATH=${STOPGAP_ADDONS_HOME}/utils:$PATH
export MATLABPATH=${STOPGAP_ADDONS_HOME}/sg_toolbox:$MATLABPATH

Lua modulefile suggestion

If you are managing your packages through Lmod, here is an idea for a modulefile definition:

local about = [==[
Description
===========
A set of utilities for enhancing the STOPGAP experience.

More information
================
    - Homepage: https://github.com/CellArchLab/stopgap-addons
]==]

help(about)
whatis(about)

depends_on("gnuplot")
depends_on("IMOD")
depends_on("STOPGAP")
-- if MATLAB module is not already loaded by STOPGAP:
-- depends_on("MATLAB")

local root = "/path/to/stopgap-addons/"

setenv("STOPGAP_ADDONS_HOME", root)
prepend_path("PATH", pathJoin(root, "bash"))
prepend_path("PATH", pathJoin(root, "utils"))
prepend_path("MATLABPATH", pathJoin(root, "sg_toolbox"))

Compatibility with different STOPGAP versions

If the variable tilesize is defined in sg_tm.cfg, stopgap_tm_parser will assume you are using STOPGAP v0.7.5 or later.

Known issues

The scripts provided here mostly lack documentation or even a proper description of the input parameters. I plan to add them over time. User at your own risk. Please open an issue if you encounter problems.