[med-svn] [ngs-sdk] 02/03: Try to catch up with previous work
Andreas Tille
tille at debian.org
Mon Feb 2 10:40:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ngs-sdk.
commit ae425c7d611ad4385189122534a0fcf9ab309e00
Author: Andreas Tille <tille at debian.org>
Date: Mon Feb 2 11:39:05 2015 +0100
Try to catch up with previous work
---
debian/control | 16 +-
debian/copyright | 4 +-
debian/docs | 1 +
debian/patches/build-system-issue-workaround.patch | 334 +++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 6 +-
6 files changed, 356 insertions(+), 6 deletions(-)
diff --git a/debian/control b/debian/control
index f5ddd15..6f8691b 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+ python-markdown
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ngs-sdk.git
Vcs-Git: git://anonscm.debian.org/debian-med/ngs-sdk.git
@@ -13,6 +14,15 @@ Package: ngs-sdk
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Next Generation Sequencing language Bindings
- NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb.
+ NGS is a new, domain-specific API for accessing reads, alignments and
+ pileups produced from Next Generation Sequencing. The API itself is
+ independent from any particular back-end implementation, and supports
+ use of multiple back-ends simultaneously. It also provides a library for
+ building new back-end "engines". The engine for accessing SRA data is
+ contained within the sister repository ncbi-vdb.
.
- The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.
+ The API is currently expressed in C++, Java and Python languages. The
+ design makes it possible to maintain a high degree of similarity between
+ the code in one language and code in another - especially between C++
+ and Java.
+
diff --git a/debian/copyright b/debian/copyright
index c76e73d..e485312 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,6 +1,6 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: <pkg>
-Source: <path_to_download>
+Upstream-Name: ngs
+Source: https://github.com/ncbi/ngs/releases
Files: *
Copyright: © 20xx-20yy <upstream>
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..daa30a3
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.html
diff --git a/debian/patches/build-system-issue-workaround.patch b/debian/patches/build-system-issue-workaround.patch
new file mode 100644
index 0000000..adf21cf
--- /dev/null
+++ b/debian/patches/build-system-issue-workaround.patch
@@ -0,0 +1,334 @@
+Description: <short summary of the patch>
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ ngs-sdk (1.0.0-1) UNRELEASED; urgency=low
+ .
+ * Initial release (Closes: #<bug>)
+Author: Andreas Tille <tille at debian.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: https://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- /dev/null
++++ ngs-sdk-1.0.0/ngs-java/Makefile.config
+@@ -0,0 +1,4 @@
++### AUTO-GENERATED FILE ###
++
++OS_ARCH = $(shell perl $(TOP)/os-arch.perl)
++include $(TOP)/./Makefile.config.$(OS_ARCH)
+--- /dev/null
++++ ngs-sdk-1.0.0/ngs-java/Makefile.config.linux.x86_64
+@@ -0,0 +1,139 @@
++### AUTO-GENERATED FILE ###
++
++OS_ARCH = $(shell perl $(TOP)/os-arch.perl)
++
++# install paths
++INST_BINDIR = /usr/bin
++INST_LIBDIR = /usr/lib
++INST_INCDIR = /usr/include
++INST_SHAREDIR = /usr/share
++INST_JARDIR = /usr/jar
++
++# build type
++BUILD = rel
++
++# target OS
++OS = linux
++OSINC = unix
++
++# prefix string for system libraries
++LPFX = lib
++
++# suffix strings for system libraries
++LIBX = a
++VERSION_LIBX = $(LIBX).$(VERSION)
++MAJMIN_LIBX = $(LIBX).$(MAJMIN)
++MAJVERS_LIBX = $(LIBX).$(MAJVERS)
++
++SHLX = so
++VERSION_SHLX = $(SHLX).$(VERSION)
++MAJMIN_SHLX = $(SHLX).$(MAJMIN)
++MAJVERS_SHLX = $(SHLX).$(MAJVERS)
++
++# suffix strings for system object files
++OBJX = o
++LOBX = pic.o
++
++# suffix string for system executable
++EXEX =
++VERSION_EXEX = $(EXEX).$(VERSION)
++MAJMIN_EXEX = $(EXEX).$(MAJMIN)
++MAJVERS_EXEX = $(EXEX).$(MAJVERS)
++
++# system architecture and wordsize
++ARCH = x86_64
++BITS = 64
++
++# tools
++JAVAC = javac
++JAVAH = javah
++JAR = jar cf
++
++# tool options
++SRCINC = -sourcepath $(INCPATHS)
++CLSPATH = -classpath $(CLSDIR)
++
++# NGS-JAVA and library version
++VERSION = 1.0.0
++MAJMIN = 1.0
++MAJVERS = 1
++
++# output path
++TARGDIR = /home/andreas/ncbi-outdir/ngs-java/linux/jdk/x86_64/rel
++
++# derived paths
++MODPATH ?= $(subst $(TOP)/,,$(CURDIR))
++SRCDIR ?= $(TOP)/$(MODPATH)
++MAKEFILE ?= $(abspath $(firstword $(MAKEFILE_LIST)))
++BINDIR = $(TARGDIR)/bin
++LIBDIR = $(TARGDIR)/jar
++ILIBDIR = $(TARGDIR)/ilib
++OBJDIR = $(TARGDIR)/obj/$(MODPATH)
++CLSDIR = $(TARGDIR)/cls
++INCPATHS = $(SRCDIR):$(SRCDIR)/itf:$(TOP)/gov/nih/nlm/ncbi/ngs
++
++# exports
++export TOP
++export MODPATH
++export SRCDIR
++export MAKEFILE
++
++# auto-compilation rules
++$(OBJDIR)/%.$(OBJX): %.cpp
++ $(CP) -o $@ $< $(CFLAGS)
++$(OBJDIR)/%.$(LOBX): %.cpp
++ $(CP) -o $@ $< $(PIC) $(CFLAGS)
++
++VPATH = $(SRCDIR)
++
++# directory rules
++$(LIBDIR) $(CLSDIR) $(INST_JARDIR):
++ mkdir -p $@
++
++# not real targets
++.PHONY: default clean install all std $(TARGETS)
++
++# dependencies
++include $(wildcard $(CLSDIR)/*.d)
++NGS_INCDIR = /home/andreas/debian-maintain/alioth/debian-med_git/ngs-sdk/ngs-sdk
++
++# installation rules
++$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 644 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_LIBX),$(LIBX),$@) $(subst .$(VERSION_LIBX),-static.$(LIBX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_LIBX),$(LIBX),$@); \
++ ln -s $(subst $(VERSION_LIBX),$(LIBX),$(@F)) $(INST_LIBDIR)$(BITS)/$(subst .$(VERSION_LIBX),-static.$(LIBX),$(@F)); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
++
++$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 755 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_SHLX),$(SHLX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_SHLX),$(SHLX),$@); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
++
++$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 755 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_EXEX),$(EXEX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_EXEX),$(EXEX),$@); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
+--- /dev/null
++++ ngs-sdk-1.0.0/ngs-sdk/Makefile.config
+@@ -0,0 +1,4 @@
++### AUTO-GENERATED FILE ###
++
++OS_ARCH = $(shell perl $(TOP)/os-arch.perl)
++include $(TOP)/./Makefile.config.$(OS_ARCH)
+--- /dev/null
++++ ngs-sdk-1.0.0/ngs-sdk/Makefile.config.linux.x86_64
+@@ -0,0 +1,150 @@
++### AUTO-GENERATED FILE ###
++
++OS_ARCH = $(shell perl $(TOP)/os-arch.perl)
++
++# install paths
++INST_BINDIR = /usr/bin
++INST_LIBDIR = /usr/lib
++INST_INCDIR = /usr/include
++INST_SHAREDIR = /usr/share
++
++# build type
++BUILD = rel
++
++# target OS
++OS = linux
++OSINC = unix
++
++# prefix string for system libraries
++LPFX = lib
++
++# suffix strings for system libraries
++LIBX = a
++VERSION_LIBX = $(LIBX).$(VERSION)
++MAJMIN_LIBX = $(LIBX).$(MAJMIN)
++MAJVERS_LIBX = $(LIBX).$(MAJVERS)
++
++SHLX = so
++VERSION_SHLX = $(SHLX).$(VERSION)
++MAJMIN_SHLX = $(SHLX).$(MAJMIN)
++MAJVERS_SHLX = $(SHLX).$(MAJVERS)
++
++# suffix strings for system object files
++OBJX = o
++LOBX = pic.o
++
++# suffix string for system executable
++EXEX =
++VERSION_EXEX = $(EXEX).$(VERSION)
++MAJMIN_EXEX = $(EXEX).$(MAJMIN)
++MAJVERS_EXEX = $(EXEX).$(MAJVERS)
++
++# system architecture and wordsize
++ARCH = x86_64
++BITS = 64
++
++# tools
++CC = gcc -c
++CP = g++ -c
++AR = ar rc
++ARX = ar x
++ARLS = ar t
++LD = gcc
++LP = g++
++
++# tool options
++DBG = -DNDEBUG
++OPT = -O3
++PIC = -fPIC
++SONAME = -Wl,-soname=$(subst $(VERSION),$(MAJVERS),$(@F))
++SRCINC = -I. -I$(SRCDIR)
++INCDIRS = $(SRCINC) -I$(TOP)
++CFLAGS = $(DBG) $(OPT) $(INCDIRS) -MD
++CLSPATH = -classpath $(CLSDIR)
++
++# NGS-SDK and library version
++VERSION = 1.0.0
++MAJMIN = 1.0
++MAJVERS = 1
++
++# output path
++TARGDIR = /home/andreas/ncbi-outdir/ngs-sdk/linux/gcc/x86_64/rel
++
++# derived paths
++MODPATH ?= $(subst $(TOP)/,,$(CURDIR))
++SRCDIR ?= $(TOP)/$(MODPATH)
++MAKEFILE ?= $(abspath $(firstword $(MAKEFILE_LIST)))
++BINDIR = $(TARGDIR)/bin
++LIBDIR = $(TARGDIR)/lib
++ILIBDIR = $(TARGDIR)/ilib
++OBJDIR = $(TARGDIR)/obj/$(MODPATH)
++CLSDIR = $(TARGDIR)/cls
++
++# exports
++export TOP
++export MODPATH
++export SRCDIR
++export MAKEFILE
++
++# auto-compilation rules
++$(OBJDIR)/%.$(OBJX): %.c
++ $(CC) -o $@ $< $(CFLAGS)
++$(OBJDIR)/%.$(LOBX): %.c
++ $(CC) -o $@ $< $(PIC) $(CFLAGS)
++$(OBJDIR)/%.$(OBJX): %.cpp
++ $(CP) -o $@ $< $(CFLAGS)
++$(OBJDIR)/%.$(LOBX): %.cpp
++ $(CP) -o $@ $< $(PIC) $(CFLAGS)
++
++VPATH = $(SRCDIR)
++
++# directory rules
++$(BINDIR) $(LIBDIR) $(ILIBDIR) $(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):
++ mkdir -p $@
++
++# not real targets
++.PHONY: default clean install all std $(TARGETS)
++
++# dependencies
++include $(wildcard $(OBJDIR)/*.d)
++
++# installation rules
++$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 644 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_LIBX),$(LIBX),$@) $(subst .$(VERSION_LIBX),-static.$(LIBX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_LIBX),$(LIBX),$@); \
++ ln -s $(subst $(VERSION_LIBX),$(LIBX),$(@F)) $(INST_LIBDIR)$(BITS)/$(subst .$(VERSION_LIBX),-static.$(LIBX),$(@F)); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
++
++$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 755 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_SHLX),$(SHLX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_SHLX),$(SHLX),$@); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
++
++$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)
++ @ echo -n "installing '$(@F)'... "
++ @ if cp $^ $@ && chmod 755 $@; \
++ then \
++ rm -f $(subst $(VERSION),$(MAJVERS),$@) $(subst $(VERSION_EXEX),$(EXEX),$@); \
++ ln -s $(@F) $(subst $(VERSION),$(MAJVERS),$@); \
++ ln -s $(subst $(VERSION),$(MAJVERS),$(@F)) $(subst $(VERSION_EXEX),$(EXEX),$@); \
++ echo success; \
++ else \
++ echo failure; \
++ false; \
++ fi
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c210bcf
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+build-system-issue-workaround.patch
diff --git a/debian/rules b/debian/rules
index 6711610..8748090 100755
--- a/debian/rules
+++ b/debian/rules
@@ -20,7 +20,11 @@
dh $@
override_dh_auto_configure:
- ./configure --prefix=/usr # --javadir=/usr/share/java
+ ./configure --prefix=/usr --javadir=/usr/share/java
+
+override_dh_auto_build:
+ dh_auto_build
+ markdown_py -f README.html README.md
#get-orig-source:
# . debian/get-orig-source
--
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