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Testing dependencies in Docker #3

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merged 6 commits into from
Nov 5, 2024
Merged

Testing dependencies in Docker #3

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335ed45
Add hello world bash script
Oct 9, 2024
00a29ac
Call dependencies in bash script
Oct 9, 2024
d515314
Pass arguments in dependency POC
Oct 15, 2024
d4bf0d3
This works!
cansavvy Oct 16, 2024
4778b3d
Install dependencies to /usr/local/bin
Oct 29, 2024
7c5c837
Add back pgPEN index
Oct 29, 2024
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47 changes: 33 additions & 14 deletions inst/extdata/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,31 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
python3-pip \
python3-dev

RUN apt-get update && apt-get -y upgrade && \
apt-get install -y build-essential wget \
libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev libcurl3-dev && \
apt-get clean && apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

Comment on lines +23 to +28
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I just moved this up so that the image layers are doing the more general / slow steps first. Just might save someone a couple minutes if they need to add a dependency later. https://docs.docker.com/get-started/docker-concepts/building-images/understanding-image-layers/

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Though looking at it now we are definitely pretty far from the most efficient dockerfile...

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Yeah, it's okay, we will polish. we're still in the stage of figuring out what is needed here.

## Put more python packages we need here
################### Install idemp ###################
ENV FOLDER=idemp
ENV DST=/usr/src

WORKDIR $DST/

RUN git clone https://github.com/yhwu/idemp.git

WORKDIR $DST/$FOLDER

RUN make && \
ln -s $DST/$FOLDER/idemp /usr/local/bin

################### Install Seqtk ###################
ENV ZIP=seqtk-1.4.tar.gz
ENV URL=https://github.com/lh3/seqtk/archive/refs/tags/v1.4.tar.gz
ENV FOLDER=seqtk-1.4
ENV DST=/home/seqtk
ENV DST=/usr/src

RUN mkdir -p $DST && \
wget $URL -O $DST/$ZIP && \
Expand All @@ -34,15 +53,15 @@ RUN mkdir -p $DST && \

WORKDIR $DST/$FOLDER

RUN make
RUN make && \
ln -s $DST/$FOLDER/seqtk /usr/local/bin

################## Install Bowtie2 ##################

ENV ZIP=bowtie2-2.4.1-linux-x86_64.zip
ENV URL=https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1
ENV FOLDER=bowtie2-2.4.1-linux-x86_64
ENV DST=/home/biodocker/bin
ENV ULOCAL=/usr/local/bin
ENV DST=/usr/local/bin

RUN mkdir -p $DST && \
wget $URL/$ZIP/download -O $DST/$ZIP && \
Expand All @@ -52,13 +71,6 @@ RUN mkdir -p $DST && \
rmdir $DST/$FOLDER

################## Install Samtools ##################

RUN apt-get update && apt-get -y upgrade && \
apt-get install -y build-essential wget \
libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev libcurl3-dev && \
apt-get clean && apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

WORKDIR /usr/src

# Samtools
Expand All @@ -67,11 +79,18 @@ RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9
rm samtools-1.9.tar.bz2 && \
cd samtools-1.9 && \
./configure --prefix $(pwd) && \
make

make && \
sudo ln -s /usr/src/samtools-1.9/samtools /usr/local/bin

################# COPY over config files
COPY config config/
COPY config /home/config/

#################### COPY scripts ###################
COPY scripts /home/scripts/

# TODO remove this once paths are not hard coded
#################### COPY data ######################
COPY data /home/data/

WORKDIR /data

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