E: Package 'libbamtools-dev' has no installation candidate

Question

[ashaneev07]

Hiii... I'm facing installation issue with augustus 3.3. During "make" it shows that ,

mkdir -p bin
cd src && make
make[1]: Entering directory `/home/dcb/Documents/sof/augustus-3.3.2/src'
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 " > cxxflags
make[1]: Leaving directory `/home/dcb/Documents/sof/augustus-3.3.2/src'
cd auxprogs && make
make[1]: Entering directory `/home/dcb/Documents/sof/augustus-3.3.2/auxprogs'
cd bam2hints; make;
make[2]: Entering directory `/home/dcb/Documents/sof/augustus-3.3.2/auxprogs/bam2hints'
g++ -Wall -O2    -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools 
bam2hints.cc:16:27: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>
                           ^
compilation terminated.
make[2]: *** [bam2hints.o] Error 1
make[2]: Leaving directory `/home/dcb/Documents/sof/augustus-3.3.2/auxprogs/bam2hints'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/dcb/Documents/sof/augustus-3.3.2/auxprogs'
make: *** [all] Error 2

When i was installing the dependency package "libbamtools-dev" , the error message was like this,

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package libbamtools-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'libbamtools-dev' has no installation candidate

My ubuntu version is 14.04. Can anyone make clarification on this? Your consideration will be a sort of great favor. Thank you.

Answer 1

[Bastien Hervé]

I think you should ask this question on stackOverflow rather than Biostars, your question is not Bioinformatics related

To answer it anyway you could try to install the library like this :

sudo apt-get install libbamtools-dev

or the answer of this guy for your library, adding a repo to your repo list of sources

https://askubuntu.com/questions/659946/package-libgeotiff-epsg-is-not-available-and-has-no-installation-candidate

Answer 2

[andrew.j.skelton73]

@Bastien definitely helps solve your compile dependency, but unless you've got a specific reason for compiling try out these resources which make it far easier to get bioinformatics software up and running!

• Bioconda - This is the best way to run on a local system, and manage lots of different software
• BioContainer - If you're more familiar with Docker / Singularity methods, or running on something restricted like a compute cluster, then this may be the more appropriate approach.