Add seqkit to the tool image

Dockerfile

@@ -35,6 +35,13 @@ RUN apt-get update && apt-get install -y gcc make wget zlib1g-dev && rm -rf /var
 COPY install_pigz.sh .
 RUN bash install_pigz.sh 2.8
 
+# SeqKit
+FROM debian:bookworm AS seqkit
+WORKDIR /build
+RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*
+COPY install_seqkit.sh .
+RUN bash install_seqkit.sh 2.13.0
+
 # Skewer
 FROM debian:bullseye AS skewer
 WORKDIR /build
@@ -64,6 +71,7 @@ COPY --from=fastqc /fastqc ./fastqc
 COPY --from=hmmer /hmmer ./hmmer
 COPY --from=pigz /pigz/ ./pigz
 COPY --from=samtools /samtools/ ./samtools
+COPY --from=seqkit /seqkit ./seqkit
 COPY --from=skewer /skewer ./skewer
 COPY --from=cdhit /cd-hit ./cd-hit
 

install_seqkit.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# Get the version from the command line argument
+version=$1
+
+# Download, extract, and install the version
+wget https://github.com/shenwei356/seqkit/releases/download/v${version}/seqkit_linux_amd64.tar.gz
+tar -xf seqkit_linux_amd64.tar.gz
+mkdir -p /seqkit/${version}
+mv seqkit /seqkit/${version}/seqkit
+chmod ugo+x /seqkit/${version}/seqkit

test.sh

@@ -118,6 +118,26 @@ for version in "${samtools_versions[@]}"; do
     fi
 done
 
+# Test SeqKit
+seqkit_versions=("2.13.0")
+
+for version in "${seqkit_versions[@]}"; do
+    seqkit_path="/tools/seqkit/${version}/seqkit"
+
+    if [ -x "$seqkit_path" ]; then
+        detected_version=$("$seqkit_path" version | head -n1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+$')
+        if [ "$detected_version" = "$version" ]; then
+            echo "SeqKit version ${version} is installed and correct."
+        else
+            echo "SeqKit version ${version} is installed but version mismatch (found $detected_version)."
+            exit 1
+        fi
+    else
+        echo "SeqKit version ${version} is not installed or not executable."
+        exit 1
+    fi
+done
+
 # Test Skewer
 skewer_versions=("0.2.2")