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Installing samtools from sourceforge

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.

installation sourceforge samtools samtools0.1.19

Hello,

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

fin swimmer

Hi fin,

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

With conda you can easily install any version you like.

*that has been packaged in to it...

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

Was there a logical reason given by them?

Did the make process complete without error?

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

2 answers

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

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

./samtools: No such file or directory

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

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

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

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