Unable to install amtools 0.1.19 during Trinity setup

[a1074938]

Having not used linux for some time I am stuck on an installation of Trinity using UBUNTU.

Trinity itself is installed and appears to be fine.

When I test the installation i get the following:

/usr/local/bin/trinityrnaseq-2.2.0$ sh ./util/support_scripts/trinity_install_tests.sh
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Performing Unit Tests of Build
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish:               has been Installed Properly
Inchworm:                has been Installed Properly
Chrysalis:               has been Installed Properly
QuantifyGraph:           has been Installed Properly
GraphFromFasta:          has been Installed Properly
ReadsToTranscripts:      has been Installed Properly
fastool:                 has been Installed Properly
parafly:                 has been Installed Properly
samtools-0.1.19 Installation appears to have FAILED

Several of these were earlier showing as failed but following forum advice I have corrected them. I am not however able to get samtools to install properly.

/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19$ make
make[1]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19'
make[2]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19'
make[2]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/bcftools'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/bcftools'
make[2]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/misc'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o  libbam.a -Lbcftools -lbcf  -lcurses  -lm -lz -lpthread
make[1]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19'
make[1]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/bcftools'
gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz -lpthread
make[1]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/bcftools'
make[1]: Entering directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/misc'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19/misc'
abab@Z800:/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19$ make install
make: *** No rule to make target 'install'. Stop.
abab@Z800:/usr/local/bin/trinityrnaseq-2.2.0/trinity-plugins/samtools-0.1.19$

I have no doubt this will have been answered elsewhere in the past but no fixes I have tried are working.

Thanks in advance.

[a1074938]

Running sudo apt install samtools:
do apt install samtools
Reading package lists... Done
Building dependency tree      
Reading state information... Done
The following NEW packages will be installed
  samtools
0 to upgrade, 1 to newly install, 0 to remove and 225 not to upgrade.
Need to get 562 kB of archives.
After this operation, 1,345 kB of additional disk space will be used.
Get:1 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 samtools amd64 0.1.19-1ubuntu1 [562 kB]
Fetched 562 kB in 0s (4,638 kB/s)
Selecting previously unselected package samtools.
(Reading database ... 180021 files and directories currently installed.)
Preparing to unpack .../samtools_0.1.19-1ubuntu1_amd64.deb ...
Unpacking samtools (0.1.19-1ubuntu1) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up samtools (0.1.19-1ubuntu1) ...

I am able to run samtools through Termianl by typing samtools which I thought meant that it was installed correctly but I still get the following when testing the installation:

 
/usr/local/bin/trinityrnaseq-2.2.0$ sh ./util/support_scripts/trinity_install_tests.sh
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Performing Unit Tests of Build
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish:               has been Installed Properly
Inchworm:                has been Installed Properly
Chrysalis:               has been Installed Properly
QuantifyGraph:           has been Installed Properly
GraphFromFasta:          has been Installed Properly
ReadsToTranscripts:      has been Installed Properly
fastool:                 has been Installed Properly
parafly:                 has been Installed Properly
samtools-0.1.19 Installation appears to have FAILED

[Germán Meléndrez Carballo]

I cannot find your error log very informative. Could you please enter into the Trinity/trinity-plugins/samtools and type "make clean", followed by "make" and paste the output it generated?

Remeber that Trinity comes with some tools packed together wit it, some of those tools are: samtools, fastool, htslib (this is actually a library used by samtools), and others more. You have installed samtools in your system, but when installing Trinity, it will try to compile the samtools that comes together with Trinity.

Please try and let me see the error log, if not, we can try a solution that can also works for you (at least worked for me), but is a little difficult.

Hope that helps.

Best

~g