UNIX for Dummies Questions & Answers

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:

Code:

export SPIDER_DIR= "/Users/username/spider" 
export SPBIN_DIR=  "$/Users/username/spider/bin/" 
export SPMAN_DIR=  "$/Users/username/spider/man/" 
export SPPROC_DIR= "$/Users/username/spider/proc/" 
export PATH="${/Users/blancacarbajal/spider}/bin:${PATH}"

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

.bashrc resides in your home directory and it's responsible for defining your environment. ${PATH} is your default path used whenever you try to execute something. Do this command

Code:

echo ${PATH}

to see what your default path is. Anything in a bracket preceded by a $ means a shell variable. You don't actually need the bracket, so ${PATH} is equivalent to $PATH. The standard is to use a bracket. What is a bit curious is the $ sign in some of the variables you are defining. Where did you actually install the spider program?

I downloaded it as a tar.gz file from the software's website (google spider single particle and you will find the website) and it was downloaded to my desktop. I unpacked it and then copied that folder into my home directory. All of the $ signs are there because the website's installation instructions said to copy that info into my bashrc file with the appropriate directories. I kind of remember from my use of Linux RedHat in the past that $ signs are used for notes, i.e. won't be read as commands??? I don't know...

As I listed above /Users/username/spider : this means it is in my home directory and the spider folder contains all the executable files. The original instructions showed the following:

" Using the 'bash' shell:
export SPIDER_DIR= "PARENT_DIR/spider"
export SPBIN_DIR= "$SPIDER_DIR/bin/"
export SPMAN_DIR= "$SPIDER_DIR/man/"
export SPPROC_DIR= "$SPIDER_DIR/proc/"
export PATH= "${SPIDER_DIR}/bin:${PATH}"

Note: Do not use a ~username construct in the SPIDER_DIR path or SPIDER will be unable to find the Results file naming script.

Finally rename the desired spider_linux executable in PARENT_DIR/spider/bin to: spider for easy access. "


I just tried to copy that information above into a text tile and replaced the PARENT/DIR with the pwd that contains the spider folder. Does that help?

---------- Post updated at 01:04 PM ---------- Previous update was at 11:02 AM ----------

So I can remove the brackets, right?

---------- Post updated 04-22-14 at 11:59 AM ---------- Previous update was 04-21-14 at 01:04 PM ----------

Hello? Anyone?

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Did you actually try it? It should work with the brackets.

You do not need to replace ${PATH} with anything, in short. ${PATH} is already defined. The SPIDER instructions just add one more string to the ${PATH} variable.

I'm sorry about that;I just felt like my question wasn't really being answered and I just being given extraneous technical information.

So is the following fine as it is as my .bashrc?:

export SPIDER_DIR= "/Users/username/spider"
export SPBIN_DIR= "$/Users/username/spider/bin/"
export SPMAN_DIR= "$/Users/username/spider/man/"
export SPPROC_DIR= "$/Users/username/spider/proc/"
export PATH= “${PATH}/bin:${PATH}"

Because I try this and I still get "command not found" when I try to run spider.