diff --git a/Dockerfile b/Dockerfile index 59ec475..95793bd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,9 +7,8 @@ LABEL about.license="GPLv3" ARG DEBIAN_FRONTEND=noninteractive #install basic libraries and python -#this is useful for having all the dependencies for which no official docker exist -#odgi is out there -#pggb same +#this is useful for having control on all the depenendencies +#odgi and pggb are excluded here WORKDIR /opt @@ -51,8 +50,6 @@ ENV PATH="/root/.cargo/bin:${PATH}" #and update RUN rustup update - -#and pgr-tk dependency RUN cargo install --locked maturin #install numpy @@ -60,7 +57,8 @@ RUN pip3 install numpy \ pandas \ matplotlib \ scikit-learn \ - scipy + scipy \ + pyfaidx #ln python to python3 -not used right now but, who knows? RUN ln -s /usr/bin/python3 /usr/bin/python @@ -99,9 +97,17 @@ RUN wget https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x ENV PATH /opt/minimap2-2.28_x64-linux:$PATH +##install bedtools + +RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static \ + && chmod +x bedtools.static \ + && mv bedtools.static bedtools + +ENV PATH /opt:$PATH + ##install gafpack ##checkout to a specific version -##we need to git bisect in order to understand what is not working properly with the newest version +##we need to git bisect in order to understand what is not working properly with the newest version - git bisect (?) RUN git clone https://github.com/ekg/gafpack.git \ && cd gafpack \ @@ -118,6 +124,15 @@ RUN git clone https://github.com/ekg/gfainject.git \ ENV PATH /opt/gfainject/target/release:$PATH +##install impg + +RUN git clone https://github.com/ekg/impg.git \ + && cd impg \ + && cargo install --force --path . + +ENV PATH /opt/impg/target/release:$PATH + + ##install cosigt RUN git clone https://github.com/davidebolo1993/cosigt.git \ @@ -126,4 +141,4 @@ RUN git clone https://github.com/davidebolo1993/cosigt.git \ && go mod tidy \ && go build cosigt -ENV PATH /opt/cosigt:$PATH \ No newline at end of file +ENV PATH /opt/cosigt:$PATH