[rhinoceros]

How can I address this problem or how do I know that the folder is not right one??

ls -l

Do you see samtools-0.1.19.tar.bz2? If not, it's not the correct folder/directory. You have to either cd to the directory into which you downloaded samtools-0.1.19.tar.bz2, or alternatively, provide full path of the file for tar (it doesn't just magically know where the file is, but always assumes current working directory..). You have a long way ahead of you

[mastal]

How to install samtools on MAC OS X?

Hi Mastal,
thank you for your answer.

Giving the command line you mentioned results in the following

tar: Option f requires an argument
Usage:
List: tar -tf <archive-filename>
Extract: tar -xf <archive-filename>
Create: tar -cf <archive-filename> [filenames...]
Help: tar --help

OK, so it seems that 'tar' is working.

What happens if you type 'tar jtvf ./samtools-0.1.19.tar.bz2'?

[Mariel_Oyervides]

Install samtools

Hi there!
I'm having problems too with the Samtools installation in my Mac. I have downloaded Xcode, also home-brew and the command line tools are installed. I've tried moving the carpet to the desk and still nothing happens. This is the message I've got from the terminal when I try to install it, I don't know what to do next.

MacBook-Pro-de-Marielownloads Mariel$ install samtools
usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 file2
install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 ... fileN directory
install -d [-v] [-g group] [-m mode] [-o owner] directory ...

Hope someone could help me

[dpryan]

Did you already download the source code, extract it, and compile it? The install command mostly moves files around and sets their permissions.

[rhinoceros]

Hi there!
I'm having problems too with the Samtools installation in my Mac. I have downloaded Xcode, also home-brew and the command line tools are installed. I've tried moving the carpet to the desk and still nothing happens. This is the message I've got from the terminal when I try to install it, I don't know what to do next.

MacBook-Pro-de-Marielownloads Mariel$ install samtools
usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 file2
install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 ... fileN directory
install -d [-v] [-g group] [-m mode] [-o owner] directory ...

Hope someone could help me

After you have extracted the file you just cd into the folder and type make. This will build you samtools. After that you can use it by typing ./samtools in the folder. Alternatively you can move samtools somewhere in your path so you can call it from wherever..

[Mariel_Oyervides]

thank you

Thank you... It's working now

[selshamieh]

Installing Samtools @0.1.19

Hi All,

I have installed samtools v 0.1.18 on my mac using macports. Since I need to install the v 0.1.19, I have tried to upgrade the 0.1.18 using macports, but it didn not work :S.

I have also downloaded the v 0.1.19 and then followed the steps that you have mentioned (unzip + make command in terminal), however when I type samtools in the terminal, I still find the version 0.1.18.

May you help plz to solve this issue ?

many thanks in advance !

[rhinoceros]

I have also downloaded the v 0.1.19 and then followed the steps that you have mentioned (unzip + make command in terminal), however when I type samtools in the terminal, I still find the version 0.1.18.

May you help plz to solve this issue ?

many thanks in advance !

What happens when you type ./samtools in the folder where you compiled the program?

I bet you didn't put it into your path, whereas the version you installed through macports is in your path..

[selshamieh]

When I put : ./samtools

I have this :
samtools-0.1.19 apple$ ./samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
mpileup multi-way pileup
depth compute the depth
faidx index/extract FASTA
tview text alignment viewer
index index alignment
idxstats BAM index stats (r595 or later)
fixmate fix mate information
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates
reheader replace BAM header
cat concatenate BAMs
bedcov read depth per BED region
targetcut cut fosmid regions (for fosmid pool only)
phase phase heterozygotes
bamshuf shuffle and group alignments by name

So what should I do next ?

How to put it in the path??

[maubp]

I would find out where the current samtools is, check with this:

$ which samtools

You could then replace the old version (safe it that was also installed by you from source), or use something like $HOME/bin and ensure that is early in your $PATH setting.

[selshamieh]

The-Godfather:samtools-0.1.19 apple$ which samtools
/opt/local/bin/samtools

May you please clarfiy to me how to replace the old version ? the commands if possible..

[rhinoceros]

So what should I do next ?

How to put it in the path??

1. open terminal
2. type cd
3. type nano .bash_profile
4. add what's below to the bottom of the document (except replace the path (/xxx/xxx/xxx/samtools) wherever you put samtools.. you can type pwd in samtools dir to see, or can first move the folder somewhere more convenient so you don't delete it accidentally or something, personally I've made a dir called Software to my home.. so this kinda stuff is always at /Users/MyName/Software/xxx):

export PATH=/Users/You/Software/samtools:${PATH}

5. hold ctrl and push x -> select save with y
6. type source .bash_profile

It's now in your path. Depending on your preferences, the older samtools might override in preference this path, so maybe it would be a good idea to uninstall it via macports (don't ask me how since I never used macports).

If all this is too difficult you can always just use samtools from your folder as you already did.. by ./samtools

[selshamieh]

Removing the old version with macports was done.
I have also entered the nano .bash_profile and added export PATH=/Users/apple/downloads/samtools-0.1.19:${PATH}
then I have overwrited the file.
and went back to /downloads/samtools-0.1.19 folder and put make.
once I made the following command:
samtools view -h *cic04130.bam | awk '$3=="chr1" || /^@/' | samtools view -Sb -> onlychr1.bam.cic4130.bam

I had this result : -bash: samtools: command not found

so apparently the v0.1.19 was not correctly installed ?

[dpryan]

you'll actually need to restart the console for the new PATH to take effect. Alternatively, just run:

export PATH=/Users/apple/downloads/samtools-0.1.19:$PATH

and be things should work.

[selshamieh]

Thank you a Million rhinoceros and dpryan !

It is working now