Augustus Installation error

Question

[ashaneev07]

Hiii.... i'm facing installation issue with augustus on my ubuntu (14.04). I have installed bamtools manually for this but, showing the following error.. Thanks.

sudo make
mkdir -p bin
cd src && make
make[1]: Entering directory `/home/dcb/Documents/EV/Maker/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/EV/Maker/augustus-3.3.2/src'
cd auxprogs && make
make[1]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs'
cd bam2hints; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/bam2hints'
make[2]: `bam2hints' is up to date.
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/compileSpliceCands'
make[2]: `compileSpliceCands' is up to date.
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o -I=/home/dcb/Documents/EV/Maker/bamtools/include/bamtools -Iheaders -I./bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>    
                               ^
compilation terminated.
make[3]: *** [filterBam.o] Error 1
make[3]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs'
make: *** [all] Error 2

[lakhujanivijay]

Switch to conda installations if not already

1. First install miniconda using this link

   https://docs.conda.io/en/latest/miniconda.html

2. Install augustus

   conda install -c bioconda augustus 

[Philipp Bayer]

Seconding conda, if you don't want conda it's a common error message for which are numerous workarounds on the internet, see for example https://iamphioxus.org/2017/05/08/installing-augustus-with-manual-bamtools-installation/

(I also edited the code in the OP post)

[ashaneev07]

Thanks for your reply.. I've edited the makefile (filterbam/src), but again it shows the same error.

make[3]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o -I/home/dcb/Documents/EV/Maker/bamtools/include/bamtools -Iheaders -I./bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>    
                               ^
compilation terminated.
make[3]: *** [filterBam.o] Error 1

[ashaneev07]

Thanks for your reply. I also tried with conda install.But while checking with augustus it shows that

 augustus: error while loading shared libraries: libboost_iostreams.so.1.60.0: cannot open shared object file: No such file or directory

[Philipp Bayer]

conda install boost could solve this (perhaps then reinstalling augustus)