How to Install Augustus properly ?

Question

[kabir.deb]

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.

[WouterDeCoster]

Have you tried installation using bioconda?

[kabir.deb]

No, I'm using python3. Is it mandatory to use bioconda! I really don't know.

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow.

Using (bio)conda will make installation of a lot of tools much easier an painless.

[kabir.deb]

Thanks everyone, Finally I've able to install BUSCO using ANACONDA, it's really cool. Now I'm trying to do comparative genome analysis using Comparative annotation toolkit (CAT). But somewhere having lost. It will be an immense help if someone familiar with this kind of tool can suggest any good tutorial for do this.

Answer 1

[william.imart]

Install miniconda (with whichever python version you're using) and augustus will be in there If you want to run BUSCO you should intall miniconda as you'll aslo need HMM and tBLAST to run it. Once you have miniconda you'll have to run a couple easy commands to locate AUGUSTUS. There are loads of userguides explaining how to use miniconda and BUSCO