Merge branch 'feat/debian' into dev

Initial debianisation of axe. Likely to change, but here it is

.gitignore

@@ -10,3 +10,8 @@ build
 *.so
 tags
 version
+
+# debian
+version
+axe-deb
+axe-demuxer_*

CMakeLists.txt

@@ -10,7 +10,7 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 ENABLE_TESTING()
 
 IF (NOT CMAKE_BUILD_TYPE)
-	SET(CMAKE_BUILD_TYPE Release)
+        SET(CMAKE_BUILD_TYPE Release)
 ENDIF()
 
 IF (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/version")
@@ -22,25 +22,26 @@ ELSE()
 			OUTPUT_VARIABLE AXE_VERSION
 			OUTPUT_STRIP_TRAILING_WHITESPACE)
 ENDIF()
+
 MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of axe version: ${AXE_VERSION}")
 
 ###############################
 ## Find Packages and Headers ##
 ###############################
 
-# all are now handled by libqes
+# Done by libqes' CML.txt
 
 ##########################
 ## Set Compiler Options ##
 ##########################
 
 IF (CMAKE_COMPILER_IS_GNUCC)
-	SET(AXEWRN "${AXEWRN} -Woverride-init -Wnormalized=id -Wlogical-op")
-	EXECUTE_PROCESS(COMMAND ${CMAKE_C_COMPILER} -dumpversion
-			OUTPUT_VARIABLE GCC_VERSION)
-	IF (GCC_VERSION VERSION_GREATER 4.9 OR GCC_VERSION VERSION_EQUAL 4.9)
-		SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fdiagnostics-color=always")
-	ENDIF()
+        SET(AXEWRN "${AXEWRN} -Woverride-init -Wnormalized=id -Wlogical-op")
+        EXECUTE_PROCESS(COMMAND ${CMAKE_C_COMPILER} -dumpversion
+                        OUTPUT_VARIABLE GCC_VERSION)
+        IF (GCC_VERSION VERSION_GREATER 4.9 OR GCC_VERSION VERSION_EQUAL 4.9)
+                SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fdiagnostics-color=always")
+        ENDIF()
 ENDIF()
 
 # Set CFLAGS
@@ -59,13 +60,17 @@ SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${AXEWRN}")
 
 INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src
                     ${CMAKE_SOURCE_DIR}/src/datrie
+                    ${CMAKE_SOURCE_DIR}/src/libqes/src
                     ${CMAKE_SOURCE_DIR}/src/gsl)
 LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/lib)
 
-INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src/libqes/src)
 INCLUDE_DIRECTORIES(${CMAKE_BINARY_DIR})
 
+CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/src/axe_config.h.in
+               ${CMAKE_BINARY_DIR}/axe_config.h)
+
 ADD_SUBDIRECTORY(docs)
 ADD_SUBDIRECTORY(tests)
 ADD_SUBDIRECTORY(src)
+SET(LIBQES_AS_SUBMODULE True)  # stop libqes installing itself
 ADD_SUBDIRECTORY(src/libqes)

deb-clean.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+set -ex
+
+rm -f axe-demuxer*
+rm -f version
+rm -rf axe-deb

deb-make.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+set -e
+set -x
+
+test -d .git
+
+PKG_DIR=axe-deb
+SRC_DIRS="src/ docs/ tests/ CMakeLists.txt debian/ version"
+
+# grab version from changelog
+VERSION="$(head -n 1 debian/changelog  |perl -pe 's/.*\((.+)-.*/$1/')"
+
+echo $VERSION >version
+rm -rf $PKG_DIR/* axe_*.orig.tar.gz
+mkdir -p $PKG_DIR
+cp -r $SRC_DIRS $PKG_DIR
+
+
+tar czf axe-demuxer_${VERSION}.orig.tar.gz $SRC_DIRS

debian/axe-demuxer.dirs

@@ -0,0 +1,2 @@
+usr/bin
+usr/share/man/man1

debian/changelog

@@ -0,0 +1,5 @@
+axe-demuxer (0.2.1-1) UNRELEASED; urgency=medium
+
+  * Initial debian release. (Closes: #XXXXX)
+
+ -- Kevin Murray <[email protected]>  Mon, 26 Jan 2015 11:00:07 +1100

debian/compat

@@ -0,0 +1 @@
+9

debian/control

@@ -0,0 +1,18 @@
+Source: axe-demuxer
+Maintainer: Kevin Murray <[email protected]>
+Section: science
+Priority: optional
+Standards-Version: 3.9.6
+Build-Depends: debhelper (>= 9),
+	       cmake,
+               zlib1g-dev
+Homepage: https://github.com/kdmurray91/axe
+
+Package: axe-demuxer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Trie-based DNA sequencing read demultiplexer
+ AXE very rapidly selects the optimal barcode present in a sequence read, even
+ in the presence of sequencing errors. The algorithm is able to handle
+ combinatorial barcoding, barcodes of differing length, and several mismatches
+ per barcode.

debian/copyright

@@ -0,0 +1,22 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: axe
+Source: https://github.com/kdmurray91/axe
+
+Files: *
+Copyright: 2014 Kevin Murray
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

debian/rules

@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
+%:
+	dh $@ --buildsystem=cmake
+

debian/source/format

@@ -0,0 +1 @@
+3.0 (quilt)

docs/CMakeLists.txt

@@ -1,24 +1,24 @@
 FIND_PROGRAM(SPHINXBUILD sphinx-build)
 IF(SPHINXBUILD)
-	SET(ALLSPHINXOPTS -q -D latex_paper_size=a4)
-	ADD_CUSTOM_TARGET(doc_html
-		COMMAND ${SPHINXBUILD} -b html ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/html
+    SET(ALLSPHINXOPTS -q -D latex_paper_size=a4)
+    ADD_CUSTOM_TARGET(doc_html
+        COMMAND ${SPHINXBUILD} -b html ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/html
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-		)
-	ADD_CUSTOM_TARGET(doc_onehtml
-		COMMAND ${SPHINXBUILD} -b singlehtml ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/single
+        )
+    ADD_CUSTOM_TARGET(doc_onehtml
+        COMMAND ${SPHINXBUILD} -b singlehtml ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/single
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-		)
-	ADD_CUSTOM_TARGET(doc_man
-		COMMAND ${SPHINXBUILD} -b man ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/man
+        )
+    ADD_CUSTOM_TARGET(doc_man
+        COMMAND ${SPHINXBUILD} -b man ${ALLSPHINXOPTS} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/doc/man
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-		)
+        )
     ADD_CUSTOM_TARGET(doc_clean
 	COMMAND ${CMAKE_COMMAND} -E remove_directory "${CMAKE_BINARY_DIR}/doc"
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
         )
     ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_onehtml)
-    INSTALL(DIRECTORY "${CMAKE_BINARY_DIR}/doc/man/" DESTINATION "man" PATTERN ".*" EXCLUDE)
+    INSTALL(FILES ${CMAKE_BINARY_DIR}/doc/man/axe.1 DESTINATION "share/man/man1")
     SET_DIRECTORY_PROPERTIES(PROPERTY ADDITIONAL_MAKE_CLEAN_FILES doc/)
 ENDIF()
 

src/CMakeLists.txt

@@ -1,10 +1,10 @@
 # Axe library (libaxe.a)
-CONFIGURE_FILE(axe_config.h.in ${CMAKE_BINARY_DIR}/axe_config.h)
 FILE(GLOB DATRIE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/datrie/*.c)
 FILE(GLOB GSL_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/gsl/*.c)
 SET(AXELIB_SRCS ${DATRIE_SRCS} ${GSL_SRCS} axe.c)
+
 ADD_LIBRARY(axelib STATIC ${AXELIB_SRCS})
-TARGET_LINK_LIBRARIES(axelib ${AXE_DEPENDS_LIBS} qes_static)
+TARGET_LINK_LIBRARIES(axelib qes_static)
 SET_TARGET_PROPERTIES(axelib PROPERTIES OUTPUT_NAME axe)
 
 # Executable