New upstream version 3.3.2+dfsg

auxprogs/utrrnaseq/.cproject

auxprogs/utrrnaseq/.project

auxprogs/utrrnaseq/.settings/

auxprogs/utrrnaseq/Debug/src/*.d

auxprogs/utrrnaseq/Debug/src/*.o

auxprogs/utrrnaseq/Debug/utrrnaseq

auxprogs/utrrnaseq/*.gff

src/*.o

auxprogs/bam2hints/bam2hints

auxprogs/bam2hints/bam2hints.o

auxprogs/bam2wig/bam2wig

auxprogs/bam2wig/bam2wig.o

auxprogs/compileSpliceCands/compileSpliceCands

auxprogs/compileSpliceCands/compileSpliceCands.o

auxprogs/compileSpliceCands/list.o

auxprogs/filterBam/src/MatePairs.o

auxprogs/filterBam/src/PairednessCoverage.o

auxprogs/filterBam/src/SingleAlignment.o

auxprogs/filterBam/src/filterBam.o

auxprogs/filterBam/src/getReferenceName.o

auxprogs/filterBam/src/initOptions.o

auxprogs/filterBam/src/printElapsedTime.o

auxprogs/filterBam/src/sumDandIOperations.o

auxprogs/filterBam/src/sumMandIOperations.o

auxprogs/homGeneMapping/src/gene.o

auxprogs/homGeneMapping/src/genome.o

auxprogs/homGeneMapping/src/homGeneMapping

auxprogs/joingenes/jg_ios.o

auxprogs/joingenes/jg_transcript.o

auxprogs/joingenes/joingenes

auxprogs/joingenes/joingenes.o

bin/

examples/cgp/out/

include/ann.hh~

src/ann.cc~

src/augustus

src/cxxflags

src/espoca

src/etraining

src/fastBlockSearch

src/getSeq

src/load2sqlitedb

src/parser/parse.o

src/prepareAlign

src/scanner/lex.o

language: generic

sudo: required

services:

  - docker

before_install:

  - printenv | grep -E '^TRAVIS_' > .env

script:

  - docker build -t augustus .

FROM ubuntu:18.04

# Install required packages

RUN apt-get update

RUN apt-get install -y build-essential wget git autoconf

# Install dependencies for AUGUSTUS

RUN apt-get install -y libboost-iostreams-dev zlib1g-dev

RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev

RUN apt-get install -y libbamtools-dev

RUN apt-get install -y libboost-all-dev

# Install additional dependencies for htslib and samtools

RUN apt-get install -y libbz2-dev liblzma-dev

RUN apt-get install -y libncurses5-dev

# Install additional dependencies for bam2wig

RUN apt-get install -y libssl-dev libcurl3-dev

# Clone AUGUSTUS repository

RUN git clone --recursive https://github.com/Gaius-Augustus/Augustus /root/augustus

# Build bam2wig dependencies (htslib, bfctools, tabix, samtools)

RUN git clone https://github.com/samtools/htslib.git /root/htslib

WORKDIR "/root/htslib"

RUN autoheader

RUN autoconf

RUN ./configure

RUN make

RUN make install

RUN git clone https://github.com/samtools/bcftools.git /root/bcftools

WORKDIR "/root/bcftools"

RUN autoheader

RUN autoconf

RUN ./configure

RUN make

RUN make install

RUN git clone https://github.com/samtools/tabix.git /root/tabix

WORKDIR "/root/tabix"

RUN make

RUN git clone https://github.com/samtools/samtools.git /root/samtools

WORKDIR "/root/samtools"

RUN autoheader

RUN autoconf -Wno-syntax

RUN ./configure

RUN make

RUN make install

ENV TOOLDIR="/root"

# Build bam2wig

RUN mkdir /root/augustus/bin

WORKDIR "/root/augustus/auxprogs/bam2wig"

RUN make

# Build AUGUSTUS

WORKDIR "/root/augustus"

RUN make

RUN make install

# Test AUGUSTUS

RUN make test

List of changes from version 3.3.1 to 3.3.2 (until Oct 5th, 2018)

     - bugfixes in comparative augustus, utrrnaseq

     - new species Chiloscyllium punctatum (bamboo shark), Scyliorhinus torazame (cat shark), Rhincodon typus (whale shark)

     - updated comparative augustus (CGP) tutorial 

List of changes from version 3.3 to 3.3.1 (until May 8th, 2018)

     - new species pisaster (Pisaster ochraceus, ochre starfish)

     - bugfixes of sampling error in intron model and in check of

# for internal purposes:

release:

	find . -name .svn | xargs rm -rf

	find . -name "*~" | xargs rm -f

	rm -f src/makedepend.pl

	rm -r augustus-training

	rm -r auxprogs/utrrnaseq/input/human-chr19

	rm -r docs/tutorial-cgp/results/cactusout

	make clean all

	make clean

	cd config/species; rm -rf tobacco xeno1 bombus_terrestris{1,3} symsag xenoturbella meara pavar newest elegans maker2_* lizard

	rm generic/*.pbl

	cd src/parser; rm Makefile; cd -

	cd ..; tar -czf augustus-$(AUGVERSION).tar.gz augustus

	cd ..; tar -czf augustus-$(AUGVERSION).tar.gz augustus-$(AUGVERSION)

test:

	./bin/augustus --species=human --UTR=on examples/example.fa

# remove -static from src/Makefile for MAC users

# remove -g -gdb from CXXFLAGS