Installing SPIDER single particle software-help with bashrc?
Hello,
I am a Unix newbie and I need some help with getting this program up and running for work. It is a program for analyzing electron microscopy images. If you google SPIDER single particle, you will find the website with the program to download as well as the installation instructions (which I am trying to follow). Sorry, I apparently can't post links on my first post.
I unpacked and put the downloaded files into my home directory and set up a .bashrc startup file there as well. I am on Mavericks so I have used TextEdit to do this. It looks something like this:
I don't know what to to put in that last line, i.e. in place of {PATH}. I actually don't know what the "{}" brackets mean. I've tried putting in the path for the /bin directory but that doesn't seem to work, i.e. if I try to run the program in the terminal window by typing spider, nothing happens. Any help would be greatly appreciated and I can provide more information if it is needed.
Does the .bashrc file have to be in the same folder as the program files? i.e. the spider folder in this case? I have a feeling it doesn't matter and that's the whole purpose of setting the file up in the first place, but I am really quite clueless. I just name is .bashrc, right?
Thank you in advance,
Blanca
Last edited by Franklin52; 04-21-2014 at 01:39 PM..
Reason: Please use code tags for data and code samples
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LEARN ABOUT DEBIAN
gpiv_vhisto
GPIV_VHISTO(1) General Commands Manual GPIV_VHISTO(1)NAME
gpiv_vhisto - Tests PIV data by printing/displaying an histogram of the vertical particle displacements.
SYNOPSIS
gpiv_vhisto [-g] [-h | --help] [-n N] [-p | --print] [-v | --version] [filename] < stdin > stdout
DESCRIPTION
Gpiv_vhisto calculates the histogram of the vertical particle displacement distribution between minimum and maximum values.
The parameters read from the configuration resources (containing the key VALID) may be overruled by the command line options, as explained
below.
Options-g Graphical visualization of the histogram with gnuplot.
-h | --help
On-line help
-n N Override number of bins (default 10, hard coded).
-p | --print
Print parameters, command line options and eventually used input and output filenames to stdout. The output is identic of file-
name.par, in case -f is used.
-v | --version
Print version information on standard output, then exit successfully.
filename
Input PIV file. Overrides stdin and stdout. Output will be written to filename.pdf. The parameters will be written or appended to
filename.par and may be used for future use by including them in ./gpivrc.
SEE ALSO
gpivtools
NOTES
stdin and stdout has still to be implemented. [-f filename ] will be added.
AUTHOR
Gerber Van der Graaf
BUGS
The program seems to work fine with real PIV data. So far, no serious bugs have been found.
8 November 2006 GPIV_VHISTO(1)
04-21-2014
I actually don't know what the "{}" brackets mean. I've tried putting in the path for the /bin directory but that doesn't seem to work, i.e. if I try to run the program in the terminal window by typing spider, nothing happens. Any help would be greatly appreciated and I can provide more information if it is needed.