Installing Error Augustus

[BiodeB]

I was trying to install Augustus in Ubuntu 16.04. However I have followed (http://bioinf.uni-greifswald.de/augustus/binaries/README.TXT) for installation but stuck in between the steps,

-htslib -bcftools -tabix -samtools For bam2wig, these four packages must be installed from github. An installation via Ubuntu packages is not sufficient. See detailed installation & compilation instructions at auxprogs/bam2wig/README.TXT Also, the environment variable TOOLDIR (directory in which htslib, bcftools, tabix and samtools reside) must be exported: export TOOLDIR=/path/where/dependencies/reside Compiling utrrnaseq requires Boost library >Boost_1_49_0. For Ubuntu e.g. install with sudo apt-get install libboost-all-dev

sudo make

Error Output:

bam2wig.c:18:17: fatal error: sam.h: No such file or directory compilation terminated. Makefile:33: recipe for target 'bam2wig.o' failed make[2]: [bam2wig.o] Error 1 make[2]: Leaving directory '/home/ub/softwares/augustus-3.3.1/auxprogs/bam2wig' Makefile:7: recipe for target 'all' failed make[1]: [all] Error 2 make[1]: Leaving directory '/home/ub/softwares/augustus-3.3.1/auxprogs' Makefile:7: recipe for target 'all' failed make: *** [all] Error 2

Hoping for good suggestion.

[nextgenusfs]

You can look at how I did it in the docker build https://github.com/nextgenusfs/funannotate/blob/master/dockerbuild/Dockerfile-base. But I also couldn't get bam2wig to build --> but funannotate doesn't use that script. The Augustus authors rarely provide any support or help.

#first need to build bamtools
wget https://github.com/pezmaster31/bamtools/archive/v2.5.0.tar.gz
tar -zxvf v2.5.0.tar.gz
rm v2.5.0.tar.gz
mv bamtools-2.5.0 bamtools
cd bamtools
mkdir build
cd build
cmake .. 
make
sudo make install
cd /usr/include
sudo ln -f -s ../local/include/bamtools/
cd /usr/lib/
sudo ln -f -s /usr/local/lib/bamtools/libbamtools.* . 

#install augustus, change to make file to comment out bam2wig as it wouldn't build
wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz
tar -zxvf augustus-3.3.1.tar.gz
rm augustus-3.3.1.tar.gz
mv augustus-3.3.1 augustus
cd augustus
sed -i 's/  cd bam2wig; make/   #cd bam2wig; make/g' /home/linuxbrew/augustus/auxprogs/Makefile
make clean
make

[BiodeB]

Thank you so much for the suggestion. I'll surely try funannotate; I would like to enquire you that is it good for invertebrate metazoan species? Though for Augustus I was following your steps but

$ sudo ln -f -s ../local/include/bamtools/
ln: ./bamtools: cannot overwrite directory

[nextgenusfs]

Perhaps its already installed globally and properly linked. check if libbamtools.* files are symlinked into /usr/lib/ or not.

[BiodeB]

Okay, 3 files namely libbamtools.a, libbamtools.so and libbamtools.so.2.4.0 are present in the /usr/lib/

[nextgenusfs]

Okay, then you should be okay with just installing Augustus as the makefiles should then find bamtools. Just comment out the bam2wig command.

[BiodeB]

Thank you Jon, finally I'm able to install Augustus .

[chiu-shenpo]

@nextgenusfs thanks for the advice cuz i was facing the same problem while installing the Augustus.