Question: Installing samtools from sourceforge
0
gravatar for c.clarido
2.0 years ago by
c.clarido60
Netherlands/Rotterdam/Leiden University (Applied Science)
c.clarido60 wrote:

Hello community,

I am trying to install the old samtools 0.1.19 from sourceforge. I can't find any documentation how to install the program. I downloaded it and uncompressed it with tar command, then I went to the folder and read the INTALL file which states the following:

System Requirements
===================

SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.

The text-based viewer (tview) requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
the modern Linux/Unix distributions. If you do not have this library installed,
you can still compile the rest of SAMtools by manually changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.

Compilation
===========

Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
razip with `make razip'.


Installation
============

Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
a location you want (e.g. a directory in your $PATH). You may also copy
`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
that the `man' command may find the manual.

So I run the make command as suggested and tried to run the samtools command but nothing happened and I get the following:

-bash: samtools: command not found

Any suggestion how I can install it properly?

PS. I am not very good with linux jargons. PS: I am required to use this specific version of samtools and not the newer ones.

ADD COMMENTlink modified 2.0 years ago by Dhana80 • written 2.0 years ago by c.clarido60
1

Hello,

Why? You were told to update to the newest version.

fin swimmer

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by finswimmer13k

Hi fin,

Yes I asked them and I am to use this version sadly...

ADD REPLYlink written 2.0 years ago by c.clarido60

With conda you can easily install any version you like.

ADD REPLYlink written 2.0 years ago by finswimmer13k

*that has been packaged in to it...

ADD REPLYlink written 2.0 years ago by Joe18k

Yes I asked them and I am to use this version sadly...

Was there a logical reason given by them?

ADD REPLYlink written 2.0 years ago by genomax91k

Did the make process complete without error?

ADD REPLYlink written 2.0 years ago by Joe18k

yeah I believe I saw some errors, if I rerun it it will just say there is nothing to be done

ADD REPLYlink written 2.0 years ago by c.clarido60
1
gravatar for Antonio R. Franco
2.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

It is likely you don't have the samtools executable binary in the $PATH. If so, try to run it by using

./samtools

when you are in the directory containing the program

ADD COMMENTlink written 2.0 years ago by Antonio R. Franco4.5k

Thank you for the reply. I get however the following:

./samtools: No such file or directory
ADD REPLYlink written 2.0 years ago by c.clarido60
1

are you in the same directory that samtools is ? In addition... is the samtools file executable ?. You can see it by running

ls -l

You need to see an "x" at least in the first group of letters after the hyphen If not, run

chmod +x samtools
ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Antonio R. Franco4.5k

Yeah It's working! thank you! I went to the folder and typed ./samtools and showed the options

ADD REPLYlink written 2.0 years ago by c.clarido60
1
gravatar for Dhana
2.0 years ago by
Dhana80
Helsinki, Finland
Dhana80 wrote:

The samtools executable should be located with the bin folder. It should run when you run it as /bin/samtools

ADD COMMENTlink written 2.0 years ago by Dhana80
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