Bugs Files

BugsLite  release 20131008
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BugsLite - Software for analyzing 3D trajectories of microorganisms
===================================================================


This release of BugsLite contains all of the programs and command files needed to replicate the results published in:
J. Amazing Results ###, ####-####


To install the software:
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# The Fortran sources have been tested to be compiled properly by several versions of gfortran, which is
# available from  gcc.gnu.org/wiki/GFortran
# (Best to download/install binaries for gfortran, which are pre-compiled for several operating systems.)


# These instructions assume you are using a tcsh (or csh) command shell - If not, you can invoke one with:

tcsh


# Create a directory to contain the software, and set the current working directory to it:

mkdir  ~/Bugs

cd  ~/Bugs


# Use a browswer to download the  BugsLite-release20131008.tar.gz  file from  sourceforge.net/projects/bugs  into this directory.

# Unpack the tar file - creates a directory called  BugsLite-release20131008/ :

gunzip  BugsLite-release20131008.tar.gz

tar -xvf  BugsLite-release20131008.tar


# Set the current working directory to this directory:

cd  BugsLite-release20131008/


# Compile the Fortran programs, putting the executables into  ~/Bugs/bin/ :
# (This also copies the command files to the same directory.)

./bugsCompileProgs-lite.com  ../bin/


# Put this executable directory in your command path:
# (On macOS systems, use:   setenv PATH  $PATH\:/Users/`whoami`/Bugs/bin/  )
# (For best results, also put this line in your  ~/.cshrc  file.)

setenv PATH  $PATH:~/Bugs/bin/

rehash


# To test the programs using the published data:
------------------------------------------------

# Create a directory to test the programs, and set the current working directory there:

mkdir  bugsTest

cd  bugsTest


# Use a browswer to download the sampleData.tar.gz file from  sourceforge.net/projects/bugs  into this directory, and unpack it:

gunzip  sampleData.tar.gz

tar -xvf sampleData.tar


# Choose a dataset to process:

cd  sampleData/wildtype-RH


# Process the data:

bugsProcessCSV-lite.com  130117run011  wildtypeRH  TES