New upstream version 0.6.8 (22dc4a79) · Commits · Debian Med / sambamba

.gitmodules

+6 −6

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		[submodule "htslib"]
		path = htslib
		url = https://github.com/lomereiter/htslib.git
		[submodule "undeaD"]
		path = undeaD
		url = https://github.com/dlang/undeaD
		[submodule "BioD"]
		path = BioD
		url = https://github.com/biod/BioD.git
		[submodule "lz4"]
		path = lz4
		url = https://github.com/lz4/lz4.git
		[submodule "BioD"]
		path = BioD
		url = https://github.com/biod/BioD.git
		[submodule "undeaD"]
		path = undeaD
		url = https://github.com/biod/undeaD.git

.travis.yml

+1 −8

Original line number	Diff line number	Diff line
		@@ -8,15 +8,8 @@ matrix:
		include:
		- os: linux
		compiler: gcc
		addons:
		apt:
		packages:
		# Our dev environment is a more recent GNU C++
		# note that Debian liblz4-dev no longer supports LZ4 frames
		# - liblz4-dev
		- shunit2
		- os: osx
		compiler: clang
		script:
		- make
		# - make test - disable tests because shunit2 we use is older
		No newline at end of file
		- make check

INSTALL.md

+22 −5

Original line number	Diff line number	Diff line
		@@ -2,10 +2,27 @@

		## Sambamba dependencies

		* D compiler
		* gcc tool chain
		* BioD
		* htslib
		* undeaD
		* D compiler (ldc)
		* BioD (git submodule)
		* gcc tool chain (for htslib and lz4)
		* htslib (git submodule)
		* undeaD (git submodule)
		* libz
		* liblz4

		## Install Sambamba from source

		After checking out the source from github with git submodules is is
		possibleto install the build tools with GNU Guix

		guix package -i gcc gdb bash ld-wrapper ldc which python2 git

		Even better, with Guix, you can create a light-weight container in the source tree
		and run our development setup

		guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
		make clean
		make -j 4
		make check

		this way all dependencies are isolated.

Makefile

+22 −7

Original line number	Diff line number	Diff line
		# This is a minimalistic make file to build sambamba with ldc2 as per instructions on
		# https://github.com/biod/sambamba#compiling-sambamba
		#
		# Targets (64-bit):
		#
		# Linux
		# OSX
		#
		# Typical usage:
		#
		# make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib debug\|profile\|release\|static
		# make LIBRARY_PATH=~/opt/ldc2-$ver-linux-x86_64/lib debug\|profile\|release\|static
		#
		# Static release with optimization (for releases):
		#
		# make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib pgo-static
		# make LIBRARY_PATH=~/opt/ldc2-$ver-linux-x86_64/lib pgo-static
		#
		# Debug version
		#
		# make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib debug
		# make LIBRARY_PATH=~/opt/ldc2-$ver-linux-x86_64/lib debug
		#

		D_COMPILER=ldc2

		UNAME_S := $(shell uname -s)
		ifeq ($(UNAME_S),Darwin)
		SYS = OSX
		else
		SYS = LINUX
		LINK_OBJ = utils/ldc_version_info_.o
		endif

		DFLAGS = -wi -I. -IBioD -IundeaD/src -g

		DLIBS = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
		DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
		LIBS = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lrt -L-lpthread -L-lm
		LIBS = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lpthread -L-lm
		LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a
		SRC = $(wildcard main.d utils/.d thirdparty/.d cram/.d) $(wildcard undeaD/src/undead/.d) $(wildcard BioD/bio//.d BioD/bio///.d BioD/bio2/.d BioD/bio2//.d) $(wildcard sambamba/.d sambamba//.d sambamba///.d)
		OBJ = $(SRC:.d=.o) utils/ldc_version_info_.o
		@@ -49,7 +64,7 @@ htslib-static:
		cd htslib && $(MAKE)

		ldc-version-info:
		./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
		python3 ./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
		cat utils/ldc_version_info_.d

		utils/ldc_version_info_.o: ldc-version-info
		@@ -78,7 +93,7 @@ singleobj:
		# ---- Link step
		$(OUT): build-setup singleobj utils/ldc_version_info_.o
		$(info linking...)
		$(D_COMPILER) $(DFLAGS) -of=bin/sambamba bin/sambamba.o utils/ldc_version_info_.o $(LIBS)
		$(D_COMPILER) $(DFLAGS) -of=bin/sambamba bin/sambamba.o $(LINK_OBJ) $(LIBS)

		test:
		./run_tests.sh
		@@ -97,7 +112,7 @@ install:
		install -m 0755 bin/sambamba $(prefix)/bin

		clean: clean-d
		cd htslib ; make clean
		cd htslib ; $(MAKE) clean
		rm -f profile.data
		rm -f profile.raw

Makefile.guix

+9 −6

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		# GNU Guix makefile. GNU Guix is the package manager for GNU and we use it for
		# sambamba development and deployment. Normally use the standard Makefile
		# instead.
		# GNU Guix makefile. GNU Guix is the package manager for GNU and we
		# use it for sambamba development and deployment. Normally use the
		# standard Makefile instead because it compiles into a singleobj.
		#
		# To build sambamba on GNU Guix:
		#
		# make -f Makefile.guix
		# make -f Makefile.guix GUIX=~/opt/sambamba-dev-env
		#
		# run with
		#
		@@ -18,7 +18,10 @@
		#
		# The following two are modified by the Guix package:
		D_COMPILER=ldc2
		LDC_LIB_PATH=$(HOME)/.guix-profile/lib
		ifndef GUIX
		GUIX=$(HOME)/.guix-profile
		endif
		LDC_LIB_PATH=$(GUIX)/lib

		UNDEAD_PATH=../undeaD/src
		BIOD_PATH=../BioD
		@@ -31,7 +34,7 @@ RPATH = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $
		LIBS = htslib/libhts.a -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
		# LIBS = htslib/libhts.a -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
		LIBS_STATIC = $(DLIBS) htslib/libhts.a $(LDC_LIB_PATH)/liblz4.a
		SRC = $(wildcard utils/.d thirdparty/.d cram/.d) $(wildcard $(UNDEAD_PATH)/undead//.d) $(wildcard $(UNDEAD_PATH)/undead/.d) $(wildcard $(BIOD_PATH)/bio//.d $(BIOD_PATH)/bio///.d) $(wildcard sambamba/.d sambamba//.d sambamba///.d) utils/ldc_version_info_.d
		SRC = $(wildcard main.d utils/.d thirdparty/.d cram/.d) $(wildcard undeaD/src/undead/.d undeaD/src/undead//.d) $(wildcard BioD/bio//.d BioD/bio///.d BioD/bio2/.d BioD/bio2//.d) $(wildcard sambamba/.d sambamba//.d sambamba///.d)
		OBJ = $(SRC:.d=.o)
		OUT = bin/sambamba