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.
"-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.
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