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Merged
bbimber merged 7 commits into from
Jan 26, 2026
Merged

Bugfix to docker #12

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54e9308
Bugfix to docker
bbimber Jan 25, 2026
558133d
Bugfix to docker
bbimber Jan 25, 2026
8038f3a
Bugfix to docker
bbimber Jan 25, 2026
cfdd262
Bugfix to docker
bbimber Jan 25, 2026
f91838f
Bugfix to docker
bbimber Jan 26, 2026
f8b25f5
Bugfix to docker
bbimber Jan 26, 2026
59e6707
Bugfix to docker
bbimber Jan 26, 2026
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68 changes: 37 additions & 31 deletions containers/cat/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,32 +4,27 @@ ARG AUGUSTUS_COMMIT=36ae43d

#RUN add-apt-repository -y ppa:deadsnakes/ppa
RUN apt-get update \
&& apt-get install -y libcurl4-openssl-dev

RUN apt-get install -y libcurl4-gnutls-dev

RUN apt-get install --fix-missing -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev \
&& apt-get install --fix-missing -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev \
libboost-all-dev sqlite3 libsqlite3-0 libsqlite3-dev libgsl0-dev lp-solve liblpsolve55-dev libbamtools-dev wget git \
wget bedtools bamtools samtools sqlite3 libgsl0-dev libcolamd2 libcurl4-openssl-dev exonerate \
wget bedtools bamtools samtools sqlite3 libgsl0-dev libcolamd2 libcurl4-openssl-dev exonerate augustus augustus-data augustus-doc \
samtools bcftools libhdf5-dev libbigwig-dev \
&& apt-get install -y libhts-dev

# missing packages: software-properties-common
RUN apt install -y augustus augustus-data augustus-doc

## htslib
RUN git clone --recursive https://github.com/samtools/htslib.git
RUN cd htslib && make install
RUN git clone --recursive https://github.com/samtools/htslib.git \
&& cd htslib \
&& make install

## bcftools
RUN git clone https://github.com/samtools/bcftools.git
RUN cd bcftools && make
RUN git clone https://github.com/samtools/bcftools.git \
&& cd bcftools \
&& make

## samtools
RUN git clone https://github.com/samtools/samtools
RUN cd samtools \
&& make \
&& make install
RUN git clone https://github.com/samtools/samtools \
&& cd samtools \
&& make \
&& make install

## MOVE Directories INTO $HOME/tool
RUN mkdir /root/tools \
Expand Down Expand Up @@ -66,36 +61,47 @@ RUN wget -q https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v

# WiggleTools
RUN git clone https://github.com/dahlo/WiggleTools
#RUN cd WiggleTools && make \
# && cd WiggleTools && make \
# && cp /WiggleTools/bin/* /bin/

RUN conda create -y -n cat -c conda-forge -c bioconda -c defaults python=3.7 pyfasta luigi seaborn pandas \
ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \
samtools bamtools augustus exonerate wiggletools bedtools \
ucsc-fatotwobit ucsc-gff3togenepred ucsc-genepredtobed ucsc-genepredtofakepsl ucsc-bamtopsl ucsc-transmappsltogenepred \
ucsc-pslpostarget ucsc-axtchain ucsc-chainmergesort ucsc-pslmap ucsc-pslrecalcmatch ucsc-pslmappostchain \
ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \
ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain
RUN conda create -y -n cat python=3.7 \
&& echo "conda activate cat" >> ~/.bashrc

RUN source activate cat \
SHELL ["/bin/bash", "--login", "-c"]

RUN conda install -n cat -c conda-forge -c bioconda -c defaults -y \
pyfasta luigi seaborn pandas \
ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \
samtools bamtools augustus exonerate wiggletools bedtools \
ucsc-fatotwobit ucsc-gff3togenepred ucsc-genepredtobed ucsc-genepredtofakepsl ucsc-bamtopsl ucsc-transmappsltogenepred \
ucsc-pslpostarget ucsc-axtchain ucsc-chainmergesort ucsc-pslmap ucsc-pslrecalcmatch ucsc-pslmappostchain \
ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \
ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain

RUN conda activate cat \
&& python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git

RUN python3 --version

RUN source activate cat \
python3 --version \
RUN conda activate cat \
&& python3 --version

RUN mkdir -p /augustus \
&& git clone https://github.com/Gaius-Augustus/Augustus.git \
&& cp -r /Augustus/config/ /augustus/config/ \
&& mv Augustus /root/Augustus
&& mv Augustus /root/tools/Augustus

ENV AUGUSTUS_CONFIG_PATH=/augustus/config/

#COPY --from=builder /augustus/bin/* /bin/
#COPY --from=builder /augustus/scripts/* /bin/

RUN cd WiggleTools && make \
&& cp /WiggleTools/bin/* /bin/
RUN wget -O wiggletools.tar.gz https://github.com/Ensembl/WiggleTools/archive/c1daac89e3775bc8f96376fc1ed7f7e645ce168c.tar.gz \
&& tar --strip-components=1 -xzf wiggletools.tar.gz \
&& make LIBS='-lwiggletools -lBigWig -lcurl -lhts -lgsl -lgslcblas -lz -lpthread -lm -llzma'


#RUN cd WiggleTools && make \
# && cp /WiggleTools/bin/* /bin/

SHELL ["conda", "run", "--no-capture-output", "-n", "cat", "/bin/bash", "-c"]