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Author: Andreas Tille <tille@debian.org>
Last-Update: 2020-06-05
Description: use Debian packaged libminimap2 and liblemon
Forwarded: not-needed
--- a/Makefile
+++ b/Makefile
@@ -8,15 +8,15 @@ export BIN_DIR = ${ROOT_DIR}/bin
export MINIMAP2_DIR = ${ROOT_DIR}/lib/minimap2
export SAMTOOLS_DIR = ${ROOT_DIR}/lib/samtools-1.9
-export CXXFLAGS += ${LIBCUCKOO} ${INTERVAL_TREE} ${LEMON} -I${MINIMAP2_DIR}
-export LDFLAGS += -lz -L${MINIMAP2_DIR} -lminimap2
+export CXXFLAGS += ${LIBCUCKOO} ${INTERVAL_TREE} ${LEMON}
+export LDFLAGS += -lz -lminimap2
ifeq ($(shell uname -m),arm64)
export arm_neon=1
export aarch64=1
endif
-.PHONY: clean all profile debug minimap2 samtools
+.PHONY: clean all profile debug
.DEFAULT_GOAL := all
@@ -34,15 +34,13 @@ ${BIN_DIR}/flye-samtools:
make samtools -C ${SAMTOOLS_DIR} -j ${THREADS}
cp ${SAMTOOLS_DIR}/samtools ${BIN_DIR}/flye-samtools
-all: minimap2 samtools
+all:
make release -C src -j ${THREADS}
profile: minimap2 samtools
make profile -C src -j ${THREADS}
-debug: minimap2 samtools
+debug:
make debug -C src -j ${THREADS}
clean:
make clean -C src
- make clean -C ${MINIMAP2_DIR}
- make clean-all -C ${SAMTOOLS_DIR}
rm -f ${BIN_DIR}/flye-minimap2
rm -f ${BIN_DIR}/flye-samtools
--- a/setup.py
+++ b/setup.py
@@ -58,7 +58,7 @@ class MakeInstall(SetuptoolsInstall):
build_dir = os.path.join(script_dir, "bin")
install_dir = self.install_scripts
- bin_files = ['flye-modules', 'flye-minimap2', 'flye-samtools']
+ bin_files = ['flye-modules']
for file in bin_files:
if not os.path.isfile(os.path.join(build_dir, file)):
sys.exit('Error: binary not found: ' + file)
--- a/flye/polishing/alignment.py
+++ b/flye/polishing/alignment.py
@@ -23,8 +23,8 @@ from flye.six.moves import range
logger = logging.getLogger()
-MINIMAP_BIN = "flye-minimap2"
-SAMTOOLS_BIN = "flye-samtools"
+MINIMAP_BIN = "/usr/bin/minimap2"
+SAMTOOLS_BIN = "/usr/bin/samtools"
ContigInfo = namedtuple("ContigInfo", ["id", "length", "type"])
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