[med-svn] [Git][med-team/flye][master] Get the build running - needs testing, installing and checking

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / flye


Commits:
5395a042 by Andreas Tille at 2020-06-05T16:42:19+02:00
Get the build running - needs testing, installing and checking

- - - - -


4 changed files:

- debian/control
- + debian/patches/fix_makefile.patch
- + debian/patches/series
- + debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
debian/control
=====================================
@@ -9,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),
                python3-setuptools,
                liblemon-dev,
                libminimap2-dev,
-               samtools
+               samtools,
+               zlib1g-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/flye
 Vcs-Git: https://salsa.debian.org/med-team/flye.git


=====================================
debian/patches/fix_makefile.patch
=====================================
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 05 Jun 2020 15:05:08 +0200
+Description: Fix clean target in Makefile
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -63,10 +63,10 @@ main.o: main.cpp
+ 
+ 
+ clean:
+-	-rm ${repeat_obj}
+-	-rm ${sequence_obj}
+-	-rm ${assemble_obj}
+-	-rm ${polish_obj}
+-	-rm ${contigger_obj}
+-	-rm ${main_obj}
+-	-rm ${MODULES_BIN}
++	-rm -f ${repeat_obj}
++	-rm -f ${sequence_obj}
++	-rm -f ${assemble_obj}
++	-rm -f ${polish_obj}
++	-rm -f ${contigger_obj}
++	-rm -f ${main_obj}
++	-rm -f ${MODULES_BIN}


=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+fix_makefile.patch
+use_debian_packaged_libs.patch


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -0,0 +1,40 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 05 Jun 2020 15:05:08 +0200
+Description: use Debian packaged libminimap2 and liblemon
+
+--- a/Makefile
++++ b/Makefile
+@@ -8,10 +8,10 @@ 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
+ 
+-.PHONY: clean all profile debug minimap2 samtools
++.PHONY: clean all profile debug
+ 
+ .DEFAULT_GOAL := all
+ 
+@@ -29,15 +29,13 @@ ${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 ${BIN_DIR}/flye-minimap2
+-	rm ${BIN_DIR}/flye-samtools
++	rm -f ${BIN_DIR}/flye-minimap2
++	rm -f ${BIN_DIR}/flye-samtools



View it on GitLab: https://salsa.debian.org/med-team/flye/-/commit/5395a042df9e4f8d492934475caad42a20259626

-- 
View it on GitLab: https://salsa.debian.org/med-team/flye/-/commit/5395a042df9e4f8d492934475caad42a20259626
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