build(docker): build kraken2 from git

Author: mbhall88

Dockerfile

@@ -1,164 +1,54 @@
-# stage: build the Rust binary
 FROM rust:slim AS builder
 
 COPY . /nohuman
+
 WORKDIR /nohuman
 
 RUN apt update \
     && apt install -y musl-tools libssl-dev pkg-config \
     && cargo build --release \
     && strip target/release/nohuman
 
-# stage: build and patch Kraken2
 FROM ubuntu:24.04 AS kraken
 
+# for easy upgrade later. ARG variables only persist during build time.
 ARG K2VER="2.17"
 
-# install dependencies (include git so we can apply patches)
+# install dependencies and cleanup apt garbage
 RUN apt-get update && apt-get -y --no-install-recommends install \
     wget \
     ca-certificates \
     zlib1g-dev \
     make \
     g++ \
+    git \
     libgoogle-perftools-dev \
     rsync \
     cpanminus \
-    ncbi-blast+ \
-    git \
-    && rm -rf /var/lib/apt/lists/* && apt-get autoclean
+    ncbi-blast+ && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
 
 # perl module required for kraken2-build
 RUN cpanm Getopt::Std
 
-# Download Kraken2, apply patches (both Makefile+install_kraken2.sh and scripts/k2),
-# then install into the container. We initialize a temporary git repo to allow git apply.
-RUN wget https://github.com/DerrickWood/kraken2/archive/v${K2VER}.tar.gz \
-    && tar -xzf v${K2VER}.tar.gz \
-    && rm -rf v${K2VER}.tar.gz \
-    && cd kraken2-${K2VER} \
-    && git init . \
-    && git add . \
-    && git commit -m "orig kraken2" >/dev/null 2>&1 || true \
-    && cat > /tmp/0001-src-Makefile.patch <<'PATCH'
-diff --git a/src/Makefile b/src/Makefile
-index df902f3..39be19e 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,17 +1,17 @@
--CXX ?= g++
-+CXX ?= $(CXX)
- KRAKEN2_SKIP_FOPENMP ?= -fopenmp
--CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3 -fPIC
--CXXFLAGS += -DLINEAR_PROBING
--CFLAGS = -Wall -std=c99 -O0 -g3
-+CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++14 -O3 -fPIC
-+CXXFLAGS += -DLINEAR_PROBING $(LDFLAGS)
-+CFLAGS = -Wall -std=c11 -O3 -g3
- 
- .PHONY: all clean install
- 
--PROGS = estimate_capacity build_db classify dump_table lookup_accession_numbers k2mask blast_to_fasta libtax
-+PROGS = estimate_capacity build_db classify dump_table lookup_accession_numbers k2mask blast_to_fasta libtax.so
- 
- all: $(PROGS)
- 
- install: $(PROGS)
--	cp $(PROGS) "$(KRAKEN2_DIR)/"
-+	install -v -m 0755 $(PROGS) "$(KRAKEN2_DIR)"
- 
- clean:
- 	rm -f *.o $(PROGS)
-@@ -61,5 +61,5 @@ blast_to_fasta: blast_to_fasta.o blast_defline.o blast_utils.o
- 
- libtax.o: libtax.cc
- 
--libtax: taxonomy.o mmap_file.o libtax.o
-+libtax.so: taxonomy.o mmap_file.o libtax.o
- 	$(CXX) $(CXXFLAGS) -shared -o libtax.so taxonomy.o mmap_file.o libtax.o
-diff --git a/install_kraken2.sh b/install_kraken2.sh
-index 248b553..5a9a7eb 100755
---- a/install_kraken2.sh
-+++ b/install_kraken2.sh
-@@ -28,10 +28,10 @@ fi
- # Perl cmd used to canonicalize dirname - "readlink -f" doesn't work
- # on OS X.
- export KRAKEN2_DIR
--KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
-+KRAKEN2_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/libexec"
- 
- mkdir -p "$KRAKEN2_DIR"
--make -C src install
-+make -C src install CXX="$CXX" CC="$CC" -j"$CPU_COUNT"
- for file in scripts/*
- do
-   destination_file="$KRAKEN2_DIR/$(basename "$file")"
-PATCH
-    RUN cat > /tmp/0002-k2.patch <<'PATCH'
-diff --git a/scripts/k2 b/scripts/k2
-old mode 100755
-new mode 100644
-index 04160c2..7d5a574
---- a/scripts/k2
-+++ b/scripts/k2
-@@ -431,7 +431,7 @@ def download_and_process_blast_volumes(args):
-     ) as pool:
-         with open("manifest.txt", "r") as in_file:
-             tarballs = in_file.readlines()
--        f = functools.partial(
-+        wrapped_func = functools.partial(
-             wrap_with_globals, extract_blast_db_files,
-             LOG.get_queue(), LOG.get_level(),
-             SCRIPT_PATHNAME
-@@ -442,7 +442,7 @@ def download_and_process_blast_volumes(args):
-         )
-         for tarball in tarballs:
-             tarball = os.path.abspath(tarball)
--            f = pool.submit(extract_blast_db_files, tarball.strip())
-+            f = pool.submit(wrapped_func, tarball.strip())
-             extraction_futures.append(f)
-         for future in concurrent.futures.as_completed(extraction_futures):
-             result = future.result()
-@@ -4214,12 +4214,17 @@ def merge_classification_output_parallel(
-         input = list(zip(file1.readlines(), file2.readlines()))
-     input_len = len(input)
-     partition_ranges = list(range(0, input_len, int(input_len / args.threads)))
--    partition_ranges[-1] = input_len
-+    partition_ranges.append(input_len)
-     job_number = 0
-     futures = []
-+    wrapped_func = functools.partial(
-+        wrap_with_globals, merge_classification_output2,
-+        LOG.get_queue(), LOG.get_level(),
-+        SCRIPT_PATHNAME
-+    )
-     for start, end in zip(partition_ranges, partition_ranges[1:]):
-         future = pool.submit(
--            merge_classification_output2, taxonomy_pathname,
-+            wrapped_func, taxonomy_pathname,
-             input[start:end], job_number, use_names, args,
-             save_seq_names, final
-         )
-PATCH
-    RUN git apply /tmp/0001-src-Makefile.patch \
-    && git apply /tmp/0002-k2.patch \
-    && ./install_kraken2.sh /bin \
-    && cp -v scripts/* /bin/ 2>/dev/null || true \
-    && cp -v src/estimate_capacity src/build_db src/classify src/dump_table src/lookup_accession_numbers src/k2mask src/blast_to_fasta /bin/ 2>/dev/null || true \
-    && test -f src/libtax.so && cp -v src/libtax.so /usr/lib/ 2>/dev/null || true
+# DL Kraken2, unpack, and install
+RUN git clone "https://github.com/DerrickWood/kraken2.git" && \
+    cd kraken2 && \
+    git checkout f885f832c9863704638dece6c29f0fa4bc19a2e3 && \
+    ./install_kraken2.sh /bin
+
 
-# final image
 FROM ubuntu:24.04
 
 COPY --from=builder /nohuman/target/release/nohuman /bin/
 COPY --from=kraken /bin/kraken2* /bin/
 
 RUN nohuman --version && \
     nohuman --check
-
 # print help and versions
 RUN kraken2 --help && \
     kraken2-build --help && \
     kraken2 --version
 
+
 ENTRYPOINT [ "nohuman" ]