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I need to install a certain version of samtools (0.1.19) (found at https://sourceforge.net/projects/samtools/).

./configure returns "no such file..." make works correctly (from what I can tell) sudo make install returns "make: *** No rule to make target 'install'. Stop."

Different versions work fine. I'm completely lost, the readme doesn't provide any help and I am not savvy enough to detect any problems in the makefile. Any help would be greatly appreciated after hours of failed attempts...

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Really you do not need to compile this application by yourself.

It is packaged in all currently supported versions in universe pocket.
You can add this pocket with (if it is no enabled) the command:

sudo add-apt-repository universe

and then you can simply install it with:

sudo apt-get install samtools

If you really want to compile samtools, then you do not need to run ./configure script (as it does not exist), just use make:

cd ~/Downloads
wget https://vorboss.dl.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2
tar -xf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make

and you will get:

$ ./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
  • Unfortunately, I cannot find a way to install the previous version: sudo apt-get install samtools=0.1.19 Reading package lists... Done Building dependency tree Reading state information... Done E: Version '0.1.19' for 'samtools' was not found – ubuntuquestions Nov 24 '18 at 20:07
  • Also, 'universe' distribution component is already enabled for all sources. – ubuntuquestions Nov 24 '18 at 20:09
  • What is your Ubuntu version? – N0rbert Nov 24 '18 at 20:12
  • Ubuntu 18.04.1. – ubuntuquestions Nov 24 '18 at 20:18
  • 18.04 has samtools (1.7-1). So if you really want 0.1.19, then compile it as described in my answer. I have never used this software, but it is possible that 1.7-1 may replace 0.1.19 by all functionality. – N0rbert Nov 24 '18 at 20:20

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