Question: How to Install Augustus properly ?
0
gravatar for kabir.deb0353
15 months ago by
kabir.deb03530 wrote:

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.

busco geneprediction augustus • 2.0k views
ADD COMMENTlink modified 10 weeks ago • written 15 months ago by kabir.deb03530

Have you tried installation using bioconda?

ADD REPLYlink written 15 months ago by WouterDeCoster41k

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

ADD REPLYlink modified 15 months ago • written 15 months ago by kabir.deb03530

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.

ADD REPLYlink written 15 months ago by WouterDeCoster41k

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.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by kabir.deb03530
0
gravatar for william.imart
10 months ago by
william.imart0 wrote:

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

ADD COMMENTlink written 10 months ago by william.imart0
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