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install gt 1.6.3 from source #49

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Jan 10, 2024
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18 changes: 14 additions & 4 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ RUN apt-get update -qq
RUN apt-get install build-essential hmmer lua5.1 ncbi-blast+ blast2 \
unzip mummer infernal exonerate mafft fasttree \
circos libsvg-perl libgd-svg-perl python-setuptools \
libc6-i386 lib32stdc++6 lib32gcc1 netcat genometools \
libc6-i386 lib32stdc++6 lib32gcc1 netcat \
last-align libboost-iostreams-dev libgslcblas0 libgsl-dev \
libcolamd2 liblpsolve55-dev libstdc++6 aragorn tantan \
libstorable-perl libbio-perl-perl libsqlite3-dev git \
Expand All @@ -48,9 +48,16 @@ RUN cd /opt && \
make install

#
# Install GenomeTools
# Install GenomeTools from source
#
RUN apt-get install genometools --yes
ADD https://github.com/genometools/genometools/archive/refs/tags/v1.6.3.tar.gz /opt/genometools-1.6.3.tar.gz
RUN cd /opt && \
tar xzf genometools-1.6.3.tar.gz && \
cd genometools-1.6.3/ && \
make cairo=no && \
make prefix=/usr cairo=no install && \
cd .. && \
rm -f genometools-1.6.3.tar.gz

#
# get GO OBO file
Expand Down Expand Up @@ -123,6 +130,7 @@ RUN cd /opt && \
./configure --prefix=/usr && \
make && \
make install && \
cd .. && \
rm -f mummer-4.0.0rc1.tar.gz

#
Expand Down Expand Up @@ -190,7 +198,9 @@ RUN pip3 install scipy
RUN cd /opt && \
tar xzf OrthoFinder_source.tar.gz && \
cd OrthoFinder_source && \
chmod +x orthofinder.py
chmod +x orthofinder.py && \
cd .. && \
rm -f OrthoFinder_source.tar.gz

## Make sure to build with 'docker build --build-arg GM_KEY=<GM_KEY> .' to populate this arg.
ARG GM_KEY
Expand Down