Use HEREDOC

dodona-edu · Dec 12, 2024 · 5f63c60 · 5f63c60
1 parent b5849e2
commit 5f63c60
Showing 1 changed file with 34 additions and 31 deletions.
diff --git a/dodona-nextflow.dockerfile b/dodona-nextflow.dockerfile
@@ -17,37 +17,40 @@ ENV NXF_HOME="/home/runner/.nextflow"
 ENV NXF_OFFLINE="true"
 ENV FASTQC_HOME="/home/runner/.fastqc"
 
-RUN mkdir -p ~/workdir \
-    && mkdir ~/bin \
-    && pushd ~/bin \
-    && curl -fLO "https://github.com/nextflow-io/nextflow/releases/download/v$NXF_VER/nextflow" \
-    && chmod +x nextflow \
-    && mkdir -p "$NXF_HOME/framework/$NXF_VER" \
-    && curl -fLo "$NXF_HOME/framework/$NXF_VER/nextflow-$NXF_VER-one.jar" "https://www.nextflow.io/releases/v$NXF_VER/nextflow-$NXF_VER-one.jar" \
-    && curl -fLO 'https://repo1.maven.org/maven2/org/codenarc/CodeNarc/3.5.0-groovy-4.0/CodeNarc-3.5.0-groovy-4.0-all.jar' \
-    && curl -fLO 'https://github.com/awslabs/linter-rules-for-nextflow/releases/download/v0.1.0/linter-rules-0.1.jar' \
-    && curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar' \
-    && curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/1.7.36/slf4j-simple-1.7.36.jar' \
-    && printf 'java -Dorg.slf4j.simpleLogger.defaultLogLevel=error -classpath "$HOME/bin/linter-rules-0.1.jar:$HOME/bin/CodeNarc-3.5.0-groovy-4.0-all.jar:$HOME/bin/slf4j-api-1.7.36.jar:$HOME/bin/slf4j-simple-1.7.36.jar" "org.codenarc.CodeNarc" "$@"' > nextflow-linter \
-    && chmod +x nextflow-linter \
-    && popd \
-    && TMPFILE=$(mktemp) \
-    && curl -fLo "$TMPFILE" "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v$FASTQC_VER.zip" \
-    && mkdir "$FASTQC_HOME" \
-    && ln -s "$FASTQC_HOME" "$FASTQC_HOME/FastQC" \
-    && unzip "$TMPFILE" -d "$FASTQC_HOME" \
-    && rm "$TMPFILE" "$FASTQC_HOME/FastQC" \
-    && chmod +x "$FASTQC_HOME/fastqc" \
-    && ln -s "$FASTQC_HOME/fastqc" "$HOME/bin/fastqc" \
-    && pip3 install --no-cache-dir "multiqc==$MULTIQC_VER" \
-    && curl -fLo "$TMPFILE" "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$TRIMMOMATIC_VER.zip" \
-    && TMPFOLDER=$(mktemp -d) \
-    && unzip "$TMPFILE" -d "$TMPFOLDER/" \
-    && mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/trimmomatic-$TRIMMOMATIC_VER.jar" "$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar" \
-    && mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/adapters/"* "$HOME/workdir" \
-    && rm -r "$TMPFILE" "$TMPFOLDER" \
-    && printf "#!/bin/sh\njava -jar \"$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar\"" > "$HOME/bin/trimmomatic" \
-    && chmod +x "$HOME/bin/trimmomatic"
+RUN <<EOF
+    set -e
+    mkdir -p ~/workdir
+    mkdir ~/bin
+    pushd ~/bin
+    curl -fLO "https://github.com/nextflow-io/nextflow/releases/download/v$NXF_VER/nextflow"
+    chmod +x nextflow
+    mkdir -p "$NXF_HOME/framework/$NXF_VER"
+    curl -fLo "$NXF_HOME/framework/$NXF_VER/nextflow-$NXF_VER-one.jar" "https://www.nextflow.io/releases/v$NXF_VER/nextflow-$NXF_VER-one.jar"
+    curl -fLO 'https://repo1.maven.org/maven2/org/codenarc/CodeNarc/3.5.0-groovy-4.0/CodeNarc-3.5.0-groovy-4.0-all.jar'
+    curl -fLO 'https://github.com/awslabs/linter-rules-for-nextflow/releases/download/v0.1.0/linter-rules-0.1.jar'
+    curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar'
+    curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/1.7.36/slf4j-simple-1.7.36.jar'
+    printf 'java -Dorg.slf4j.simpleLogger.defaultLogLevel=error -classpath "$HOME/bin/linter-rules-0.1.jar:$HOME/bin/CodeNarc-3.5.0-groovy-4.0-all.jar:$HOME/bin/slf4j-api-1.7.36.jar:$HOME/bin/slf4j-simple-1.7.36.jar" "org.codenarc.CodeNarc" "$@"' > nextflow-linter
+    chmod +x nextflow-linter
+    popd
+    TMPFILE=$(mktemp)
+    curl -fLo "$TMPFILE" "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v$FASTQC_VER.zip"
+    mkdir "$FASTQC_HOME"
+    ln -s "$FASTQC_HOME" "$FASTQC_HOME/FastQC"
+    unzip "$TMPFILE" -d "$FASTQC_HOME"
+    rm "$TMPFILE" "$FASTQC_HOME/FastQC"
+    chmod +x "$FASTQC_HOME/fastqc"
+    ln -s "$FASTQC_HOME/fastqc" "$HOME/bin/fastqc"
+    pip3 install --no-cache-dir "multiqc==$MULTIQC_VER"
+    curl -fLo "$TMPFILE" "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$TRIMMOMATIC_VER.zip"
+    TMPFOLDER=$(mktemp -d)
+    unzip "$TMPFILE" -d "$TMPFOLDER/"
+    mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/trimmomatic-$TRIMMOMATIC_VER.jar" "$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar"
+    mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/adapters/"* "$HOME/workdir"
+    rm -r "$TMPFILE" "$TMPFOLDER"
+    printf "#!/bin/sh\njava -jar \"$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar\"" > "$HOME/bin/trimmomatic"
+    chmod +x "$HOME/bin/trimmomatic"
+EOF
 
 WORKDIR /home/runner/workdir