Installing bioinformatics software basic help (set path?)

[ronton]

I have a general question regarding dealing with bioinformatics software.

Many tools seem to have dependencies, for example in order for x to work, you must install samtools first.

For several programs, I have downloaded binaries and extracted them into /home/, for example /home/me/vcftools or /home/me/gatk.

What if a tool requires that something be installed first in order to compile and/or run? Should I be manually adding each of the directories into my PATH environment variable, or should I be moving/copying all of my executables into /bin/, or ... ?

Thank you

[GenoMax]

If you are the only user on this computer you could copy the executables to /usr/local/bin. Alternatively you can create softlinks for the executables (http://www.cyberciti.biz/faq/creatin...symbolic-link/) in a directory (/bin or /usr/bin would work if you are creating symlinks but as WhatsOEver points out below /usr/local/bin may be best if you are copying user installed executables) that is in $PATH.

[WhatsOEver]

1) In general it is bad practise to copy executables as symlinks work just as well, don't waste space and you are more flexible when you start having different versions of the same program.

2) I would definitely not consider /bin and /usr/bin as suitable places for executables from self installed software. Use the /usr/local/bin directory instead.

3) When you start working with Linux it is worth starting to get an idea of the filesystem hierarchy. Have a look here

http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard

and here

http://askubuntu.com/questions/138547/how-to-understand-the-ubuntu-file-system-layout/138551#138551

for an overview

[Sheree Yau]

Thanks very much the advice. It's very helpful for us newbies out there to be pointed on the right track.