feat: support cd-hit 4.8.1

Dockerfile

@@ -49,6 +49,12 @@ RUN apt-get update && apt-get install -y build-essential wget libbz2-dev zlib1g-
 COPY install_samtools.sh .
 RUN bash install_samtools.sh 1.22.1
 
+FROM debian:bookworm AS cdhit
+WORKDIR /build
+RUN apt-get update && apt-get install -y wget build-essential libz-dev && rm -rf /var/lib/apt/lists/*
+COPY install_cdhit.sh .
+RUN bash install_cdhit.sh 4.8.1 v4.8.1-2019-0228
+
 # Combine tools into a single image.
 FROM debian:bookworm AS combine
 WORKDIR /tools
@@ -59,6 +65,7 @@ COPY --from=hmmer /hmmer ./hmmer
 COPY --from=pigz /pigz/ ./pigz
 COPY --from=samtools /samtools/ ./samtools
 COPY --from=skewer /skewer ./skewer
+COPY --from=cdhit /cd-hit ./cd-hit
 
 # Testing
 FROM debian:bookworm AS test

install_cdhit.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Get the version from the command line argument
+version=$1
+slug=$2
+
+# Download, extract, configure, and install the version
+wget https://github.com/weizhongli/cdhit/releases/download/V${version}/cd-hit-${slug}.tar.gz
+tar -xf cd-hit-$slug.tar.gz
+cd cd-hit-$slug
+sed -i 's/LDFLAGS += -lz -o/LDFLAGS += -Wl,-Bstatic -lgomp -Wl,-Bdynamic -lz -o/' Makefile
+make && make install
+cd ..
+mkdir -p /cd-hit/${version}
+mv cd-hit-$slug/cd-hit* /cd-hit/${version}

test.sh

@@ -137,4 +137,24 @@ for version in "${skewer_versions[@]}"; do
         echo "Skewer version ${version} is not installed or not executable."
         exit 1
     fi
-done
+done
+
+# Test cd-hit
+cd_hit_versions=("4.8.1")
+
+for version in "${cd_hit_versions[@]}"; do
+    cd_hit_path="/tools/cd-hit/${version}/cd-hit"
+
+    if [ -x "$cd_hit_path" ]; then
+        detected_version=$("$cd_hit_path" | head -n 1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')
+        if [ "$detected_version" = "$version" ]; then
+            echo "cd-hit version ${version} is installed and correct."
+        else
+            echo "cd-hit version ${version} is installed but version mismatch (found $detected_version)."
+            exit 1
+        fi
+    else
+        echo "cd-hit version ${version} is not installed or not executable."
+        exit 1
+    fi
+done