More Samtools woes on mac

[nimrod337]

Okay, I finally got samtools installed (or so I think.) after downloading Xcode, and getting the make command to work. But now when I try to use samtools, I keep getting:

"-bash: samtools: command not found"

several people had recommended adding the ./ before samtools to get it to work, but when I do that, I get this:

"-bash: ./samtools: No such file or directory"

So what's the deal?
I need to be in the directory where samtools was installed, correct? so

"cd XXXXX" where XXXXX is the directory that samtools was "make" into, then
"./samtools faidx /Users/2/PGSC_DM_v3_2.1.11_pseudomolecules.fasta"

This should compile an index using the .fasta file correct? Where am I going wrong here?
I'm losing my mind here. I obviously don't have any UNIX background, but I get the jist, so if you could explain it too me as if I was your grandmother, that would really help.
Thanks guys, this website has already been so helpful.

[GenoMax]

Just to confirm that you have built samtools correctly do this:

"cd XXXXX" where XXXXX is the directory that samtools was "make" into

and run the following command and post the output here

$ pwd
$ ls -lt

As long as "samtools" was correctly built the following command will work.

$ /[COLOR="Red"]replace_with_output_from_pwd_command_above[/COLOR]/samtools faidx /User/2/PGSC_DM_v3_2.1.11_pseudomolecules.fasta

You can either go to the directory where you have samtools installed or you can run any of these programs from any other directory on your machine as long as you provide correct full (or relative) file paths.

[dpryan]

If you have anyone locally in IT, you might just offer to buy him/her a beer or coffee for a quick bit of help. It'll make your life a bit easier going forward

[nimrod337]

Okay, I just cleared everything out of my folders, and made a new one, downloaded samtools again, made it again, and it seems to be working. Now I am just waiting on it to sort. Must have been a weird pathing thing... Seems to me all Unix problems are pathing related. Thank you for your help, and ON TO THE NEXT PROBLEM!! (Tablet)

[rhinoceros]

Next you'll

cd to bamtools
pwd
cd
nano .bash_profile

and add the line

export PATH=/thePathPwdGave/samtools:${PATH}

and save

and then you can 'samtools' from wherever in terminal.

Learning to add programs into your path (as above) is highly recommend..