Samtools Mac Install

[drio]

Umm.. try:

$ /Users/jlc/desktop/samtools/samtools view /Users/jlc/desktop/samtools/my.bam

And get a Unix book

[jlc_1020]

Run this cmds and post the results here:

$ pwd
$ which samtools
$ ls -lac my_bam
$ samtools view my_bam

I entered those commands in the directory that contains the samtools executable file and this is what I get:

jlc-macbook-pro:samtools jlc$ pwd
/Users/jlc/desktop/samtools
jlc-macbook-pro:samtools jlc$ which\ samtools
-bash: which samtools: command not found
jlc-macbook-pro:samtools jlc$ ls -lac my.bam
-rw-r--r--@ 1 jlc staff 1537771973 Mar 9 09:47 my.bam
jlc-macbook-pro:samtools jlc$ samtools view my.bam
-bash: samtools: command not found

If I back up one directory and enter in the view command I get:

jlc-macbook-pro:desktop jlc$ samtools/samtools view my.bam
open: No such file or directory
[main_samview] fail to open file for reading.

[drio]

When I enter that code, I get a summary of the program information:

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.7-6 (r530)

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
pileup generate pileup output
faidx index/extract FASTA
tview text alignment viewer
index index alignment
fixmate fix mate information
glfview print GLFv3 file
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates

But when I try to add samtools commands, like "samtools view XXXX.bam" i get:

open: No such file or directory
[main_samview] fail to open file for reading.

Run this cmds and post the results here:

$ pwd
$ which samtools
$ ls -lac my_bam
$ samtools view my_bam

[jlc_1020]

When I enter that code, I get a summary of the program information:

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.7-6 (r530)

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
pileup generate pileup output
faidx index/extract FASTA
tview text alignment viewer
index index alignment
fixmate fix mate information
glfview print GLFv3 file
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates

But when I try to add samtools commands, like "samtools view XXXX.bam" i get:

open: No such file or directory
[main_samview] fail to open file for reading.

[dawe]

I prefer to compile on my own, nevertheless you should be able to run this

~/Deskop/samtoolsXXXX/samtools

where samtoolsXXXX is the directory containing the samtools executable...
Can you post the error you get?

d

[jlc_1020]

I'm new to Unix and starting in a Bioinformatics Lab

I recently got some .bam files from a collaborator and am trying
to get samtools running on my Macbook Pro.

I downloaded the samtools-0.1.7_i386-darwin.tar.bz2 file from their
site and extracted it to the desktop. So far I've been unsuccessful in
my efforts to get the program running in Terminal from this point.

Can anyone help point me in the right direction?

Thanks