cannot configure or make install samtools 0.1.19
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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...
make configure
asked Nov 24 at 18:21
ubuntuquestions
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up vote
1
down vote
favorite
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...
make configure
asked Nov 24 at 18:21
ubuntuquestions
82
New contributor
ubuntuquestions is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
up vote
1
down vote
favorite
up vote
1
down vote
favorite
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...
make configure
asked Nov 24 at 18:21
ubuntuquestions
82
New contributor
ubuntuquestions is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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...
make configure
make configure
asked Nov 24 at 18:21
ubuntuquestions
82
New contributor
ubuntuquestions is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked Nov 24 at 18:21
ubuntuquestions
82
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ubuntuquestions is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked Nov 24 at 18:21
ubuntuquestions
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ubuntuquestions is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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asked Nov 24 at 18:21
ubuntuquestions
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asked Nov 24 at 18:21
ubuntuquestions
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82
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1 Answer
1
active
oldest
votes
up vote
0
down vote
accepted
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
answered Nov 24 at 18:47
N0rbert
19.7k54392
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
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
answered Nov 24 at 18:47
N0rbert
19.7k54392
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
add a comment |
up vote
0
down vote
accepted
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
answered Nov 24 at 18:47
N0rbert
19.7k54392
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
add a comment |
up vote
0
down vote
accepted
up vote
0
down vote
accepted
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
answered Nov 24 at 18:47
N0rbert
19.7k54392
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
answered Nov 24 at 18:47
N0rbert
19.7k54392
edited Nov 24 at 19:00
answered Nov 24 at 18:47
N0rbert
19.7k54392
answered Nov 24 at 18:47
N0rbert
19.7k54392
answered Nov 24 at 18:47
N0rbert
19.7k54392
19.7k54392
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
add a comment |
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
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 at 20:07
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 at 20:07
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
Also, 'universe' distribution component is already enabled for all sources.
– ubuntuquestions
Nov 24 at 20:09
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
What is your Ubuntu version?
– N0rbert
Nov 24 at 20:12
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 at 20:18
Ubuntu 18.04.1.
– ubuntuquestions
Nov 24 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 at 20:20
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 at 20:20
add a comment |
ubuntuquestions is a new contributor. Be nice, and check out our Code of Conduct.
ubuntuquestions is a new contributor. Be nice, and check out our Code of Conduct.
ubuntuquestions is a new contributor. Be nice, and check out our Code of Conduct.
ubuntuquestions is a new contributor. Be nice, and check out our Code of Conduct.
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