Commit 3edf606c authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 3.3.3+dfsg

parent faf2de90

.gitignore

+1 −0
Original line number Diff line number Diff line
@@ -6,6 +6,7 @@ auxprogs/utrrnaseq/Debug/src/*.o 
auxprogs/utrrnaseq/Debug/utrrnaseq

auxprogs/utrrnaseq/*.gff

src/*.o

src/googletest/*.o

auxprogs/bam2hints/bam2hints

auxprogs/bam2hints/bam2hints.o

auxprogs/bam2wig/bam2wig

.travis.yml

+32 −1
Original line number Diff line number Diff line 
language: generic



matrix:

  include:

  - os: linux

    dist: xenial

    sudo: required

  - os: linux

    dist: trusty

    sudo: required



sudo: required



addons:

  apt:

    packages:

      - doxygen

      - doxygen-doc

      - doxygen-latex

      - doxygen-gui

      - graphviz



services:

  - docker
@@ -8,4 +27,16 @@ before_install: 
  - printenv | grep -E '^TRAVIS_' > .env

  

script:

  - docker build -t augustus .
 
  - docker build -f Dockerfile -t augustus .

  - docker build -f Dockerfile-cgp-file -t augustus-cgp-file .

  - docker build -f Dockerfile-cgp-mysql -t augustus-cgp-mysql .

  - docker build -f Dockerfile-cgp-sqlite -t augustus-cgp-sqlite .

  - doxygen doxygen.conf



deploy:

  provider: pages

  skip-cleanup: true

  local-dir: $TRAVIS_BUILD_DIR/doxygen/html

  github-token: $GITHUB_API_KEY

  on:

    branch: master

Dockerfile

+6 −8
Original line number Diff line number Diff line
@@ -18,10 +18,7 @@ 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)

# Build bam2wig dependencies (htslib, bfctools, samtools)

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

WORKDIR "/root/htslib"

RUN autoheader
@@ -36,9 +33,6 @@ 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
@@ -48,8 +42,11 @@ RUN make 
RUN make install

ENV TOOLDIR="/root"



# Clone AUGUSTUS repository

ADD / /root/augustus



# Build bam2wig

RUN mkdir /root/augustus/bin

RUN mkdir -p /root/augustus/bin

WORKDIR "/root/augustus/auxprogs/bam2wig"

RUN make
@@ -57,6 +54,7 @@ RUN make 
WORKDIR "/root/augustus"

RUN make

RUN make install

ENV PATH="/root/augustus/bin:${PATH}"



# Test AUGUSTUS

RUN make test

Dockerfile-cgp-file

0 → 100644
+64 −0
Original line number Diff line number Diff line 
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



# Build bam2wig dependencies (htslib, bfctools, 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/samtools.git /root/samtools

WORKDIR "/root/samtools"

RUN autoheader

RUN autoconf -Wno-syntax

RUN ./configure

RUN make

RUN make install

ENV TOOLDIR="/root"



# Clone AUGUSTUS repository

ADD / /root/augustus



WORKDIR "/root/augustus"



RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk



# Build bam2wig

RUN mkdir -p /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

Dockerfile-cgp-mysql

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+64 −0
Original line number Diff line number Diff line 
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



# Build bam2wig dependencies (htslib, bfctools, 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/samtools.git /root/samtools

WORKDIR "/root/samtools"

RUN autoheader

RUN autoconf -Wno-syntax

RUN ./configure

RUN make

RUN make install

ENV TOOLDIR="/root"



# Clone AUGUSTUS repository

ADD / /root/augustus



RUN sed -i "s/#.*MYSQL = true/MYSQL = true/g" /root/augustus/common.mk

RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk



# Build bam2wig

RUN mkdir -p /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