Samtools Mac Install

[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

[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]

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.

[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]

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]

Umm.. try:

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

And get a Unix book

[jlc_1020]

Umm.. try:

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

And get a Unix book

Same error message:

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

Thanks though

[lparsons]

From the samtools directory, try:

./samtools view my.bam

[jlc_1020]

I figured it out. It was a problem with the directory where my files were located. I moved them to a new directory and it worked fine.

[raiseal]

using samtools with mac

could you post the directory that you installed samtools into in order to get it to work? I have this problem too.

[adamdeluca]

quick tip for mac users, if you drag a file into a terminal window the full path will appear.

It does not matter where you install samtools, you just need to provide the correct path to the executable, and the input files.

[jlc_1020]

I installed samtools in a folder on the desktop and then put my files in the home folder so I wouldn't have to specify a path to them (since terminal is automatically in the home folder when it opens). To run, I used:

desktop/samtools/samtools view myfile.bam

[maivantan]

Any one can suggest me about below problem

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
[fai_load] build FASTA index.
-bash: bcftools: command not found
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

Thank you very much

[GenoMax]

If you built samtools on this computer then "bcftools" program is generally present in its own directory (also called "bcftools" btw). You can either add these directories to your $PATH or provide the full path to the bcftools executable in your command line.

[maivantan]

i provided full path of bcftools as bellowing

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | User/user/tan_analysis/samtools-0.1.19/bcftools view -bvcg - > eg2.raw.bcf
-bash: User/user/tan_analysis/samtools-0.1.19/bcftools: No such file or directory
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

but the same problem i got.
Please give suggestion
Thank you