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docker build updates #3

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merged 7 commits into from
Dec 12, 2023
Merged

docker build updates #3

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5f39323
switch to installing reconstructR from files here instead of repo
dpark01 Dec 12, 2023
e1d81e0
fix typo
dpark01 Dec 12, 2023
47575f4
add a cp_and_decompress script
dpark01 Dec 12, 2023
d775a66
add pigz via apt
dpark01 Dec 12, 2023
5e64745
whitespace
dpark01 Dec 12, 2023
4708cec
add multi-file version
dpark01 Dec 12, 2023
de9e8b8
merge apt-get update and apt-get install build layers -- install will…
dpark01 Dec 12, 2023
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16 changes: 7 additions & 9 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,14 @@ LABEL maintainer "Daniel Park <[email protected]>"
# non-interactive session just for build
ARG DEBIAN_FRONTEND=noninteractive

# update apt database and install R apt repo
# update apt database and install R apt repo; install all desired packages
RUN apt-get update && \
apt-get -y -qq install software-properties-common && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/' && \
apt-get update

# install all desired packages
RUN apt-get -y -qq install \
less nano vim git wget curl jq zstd parallel locales \
apt-get update && \
apt-get -y -qq install \
less nano vim git wget curl jq zstd pigz parallel locales \
gnupg libssl-dev libcurl4-openssl-dev \
libgsl-dev libxml2 libxml2-dev \
imagemagick libmagick++-dev \
Expand All @@ -35,9 +33,9 @@ RUN R -e "for (lib in c( 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect'
# Rfast in CRAN is broken, install from github
RUN R -e "devtools::install_github('RfastOfficial/Rfast', dependencies=TRUE); library(Rfast)"

# Install reconstructR R package -- invalidate cache any time github main branch updates
ADD https://api.github.com/repos/broadinstitute/reconstructR/git/refs/heads/main version.json
RUN R -e "devtools::install_github('broadinstitute/reconstructR', dependencies=TRUE, upgrade='never'); library(reconstructR)"
# Install reconstructR R package
COPY . /opt/reconstructR
RUN R -e "devtools::install_local('/opt/reconstructR', dependencies=TRUE, upgrade='never'); library(reconstructR)"

# Bash prompt
CMD ["/bin/bash"]
12 changes: 12 additions & 0 deletions scripts/cp_and_decompress.sh
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@@ -0,0 +1,12 @@
#!/bin/bash

INFILE=$1
OUTFILE=$2

if [[ $INFILE == *.gz ]]; then
pigz -dc $INFILE > $OUTFILE
elif [[ $INFILE == *.zst ]]; then
zstd -d $INFILE -o $OUTFILE
else
cp $INFILE $OUTFILE
fi
17 changes: 17 additions & 0 deletions scripts/mcp_and_decompress.sh
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@@ -0,0 +1,17 @@
#!/bin/bash

INFILES=${@:1:$#-1}
OUTDIR=${@:$#}

for INFILE in $INFILES; do
if [[ $INFILE == *.gz ]]; then
OUTFNAME=$(basename $INFILE .gz)
pigz -dc $INFILE > "$OUTDIR/$OUTFNAME"
elif [[ $INFILE == *.zst ]]; then
OUTFNAME=$(basename $INFILE .zst)
zstd -d $INFILE -o "$OUTDIR/$OUTFNAME"
else
OUTFNAME=$(basename $INFILE)
cp $INFILE "$OUTDIR/$OUTFNAME"
fi
done
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