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New Base Image added for use in Dockerfile #253

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New Base Image added for use in Dockerfile #253

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24 changes: 13 additions & 11 deletions containers/serraplace/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,18 +1,20 @@
FROM ubuntu:18.04
##### Builder Image #######
FROM base_img_serratus:latest
# install all the dependencies
RUN apt-get update &&\
apt-get -y install wget git cmake build-essential zlib1g-dev gzip unzip flex bison &&\
wget http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz&& tar xzvf hmmer-3.3.tar.gz && cd hmmer-3.3/ &&\
./configure && make -j4 && make install && cd easel && make install && cd ../../ &&\
git clone --recursive https://github.com/Pbdas/epa-ng.git &&\
cd epa-ng && git checkout tags/v0.3.7 && git submodule update --init --recursive && make -j4 && cp bin/epa-ng /usr/local/bin && cd - &&\
git clone https://github.com/lh3/seqtk.git && cd seqtk && make && cp seqtk /usr/local/bin && cd - &&\
RUN apk add cmake bison flex zlib-dev && git clone --recursive https://github.com/Pbdas/epa-ng.git &&\
cd epa-ng && git checkout tags/v0.3.7 && git submodule update --init --recursive && make -j4 && cd - &&\
git clone https://github.com/lh3/seqtk.git && cd seqtk && make && cd - &&\
git clone --recursive https://github.com/lczech/gappa.git &&\
cd gappa && git checkout f05e9fe && git submodule update --init --recursive && make -j4 && cp bin/gappa /usr/local/bin && cd - &&\
cd gappa/libs/genesis/apps && git clone https://github.com/Pbdas/genesis-apps.git && make -j4 -C .. && cp ../bin/apps/genesis-apps/msa-merge ../bin/libgenesis.so /usr/local/bin && cd - &&\
mkdir -p /serratus-data/serraplace && cd /serratus-data/serraplace && wget https://serratus-public.s3.amazonaws.com/pb/serraplace/reference/refpack.tar.gz && tar xzvf refpack.tar.gz && cd -
cd gappa && git checkout f05e9fe && git submodule update --init --recursive && make -j4 && cd - &&\
cd gappa/libs/genesis/apps && git clone https://github.com/Pbdas/genesis-apps.git && make -j4 -C .. && cd -

####### Final Image #########

FROM base_img_serratus:latest
WORKDIR /home/serratus
COPY --from=builder epa-ng/bin/epa-ng /usr/local/bin
COPY --from=builder seqtk/seqtk /usr/local/bin
COPY --from=builder gappa/libs/genesis/bin/gappa gappa/libs/genesis/bin/libgenesis.so /usr/local/bin
COPY place.sh /home/serratus/

ENTRYPOINT ["/home/serratus/place.sh", "-d"]
7 changes: 7 additions & 0 deletions containers/serraplace/Dockerfile_BaseImg
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FROM alpine:latest
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This was a very large rabbit-hole in the early days of Serratus development, but Alpine Linux is not the preferred distribution for a lightweight deployment. The C compiler (musl) ended up throwing weird errors when building some bioinformatics software.

For lightweight build the go to distro has been amazonlinux:2. This will make it more consistent with the rest of the project.

# install all the dependencies
RUN apk add --update alpine-sdk && apk add wget git cmake unzip &&\
wget http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz && tar xzvf hmmer-3.3.tar.gz && cd hmmer-3.3/ &&\
./configure && make -j4 && make install && cd easel && make install && cd ../../ &&\
mkdir -p /serratus-data/serraplace && cd /serratus-data/serraplace && wget https://serratus-public.s3.amazonaws.com/pb/serraplace/reference/refpack.tar.gz && tar xzvf refpack.tar.gz &&\
rm refpack.tar.gz && cd -