[med-svn] [transrate-tools] 02/02: initial packaging
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Sep 19 01:32:20 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository transrate-tools.
commit 8f199a4da28b00ed4182d88ce4d7ffbb4faa17c9
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Fri Sep 18 17:37:08 2015 -0700
initial packaging
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 18 ++++++++++
debian/copyright | 11 ++++++
debian/patches/cmake-bamtools | 77 ++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 22 ++++++++++++
debian/source/format | 1 +
debian/transrate-tools.install | 1 +
debian/upstream/metadata | 12 +++++++
debian/watch | 15 ++++++++
11 files changed, 164 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d1691cd
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+transrate-tools (1.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Fri, 18 Sep 2015 17:38:02 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..7497cdc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,18 @@
+Source: transrate-tools
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Build-Depends: debhelper (>= 9),
+ cmake,
+ libbamtools-dev
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: https://github.com/Blahah/transrate-tools
+
+Package: transrate-tools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: helper for transrate
+ <long_description>
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..182fe6f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: transrate-tools
+Source: https://github.com/Blahah/transrate-tools
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2014 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/patches/cmake-bamtools b/debian/patches/cmake-bamtools
new file mode 100644
index 0000000..e358d05
--- /dev/null
+++ b/debian/patches/cmake-bamtools
@@ -0,0 +1,77 @@
+--- transrate-tools.orig/CMakeLists.txt
++++ transrate-tools/CMakeLists.txt
+@@ -19,11 +19,13 @@
+
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+-SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)
++#SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)
+
+ ## Set the standard required compile flags
+ set (CMAKE_CXX_FLAGS "-fPIC -O3 -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DHAVE_CONFIG_H -Wall -std=c++11")
+-set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++
++find_package(bamtools REQUIRED)
+
+ ##
+ # Record this top-level path
+@@ -33,14 +35,14 @@
+ # Have CMake tell us what it's doing
+ set (CMAKE_VERBOSE_MAKEFILE true)
+
+-if("${CMAKE_SYSTEM}" MATCHES "Linux")
+- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-endif("${CMAKE_SYSTEM}" MATCHES "Linux")
++#if("${CMAKE_SYSTEM}" MATCHES "Linux")
++# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#endif("${CMAKE_SYSTEM}" MATCHES "Linux")
+
+ if(APPLE)
+ find_package (ZLIB REQUIRED)
+ else()
+- find_package (ZLIB REQUIRED STATIC)
++ find_package (ZLIB REQUIRED)
+ endif()
+
+ # Recurse into transrate-tools source directory
+--- transrate-tools.orig/src/CMakeLists.txt
++++ transrate-tools/src/CMakeLists.txt
+@@ -2,13 +2,9 @@
+ set(BAMREAD_HEADERS pileup.h segmenter.h)
+
+
+-include_directories(${GAT_SOURCE_DIR}/bamtools/include)
+-link_directories(${GAT_SOURCE_DIR}/bamtools/lib)
+-
+-set(LIBRARIES ${GAT_SOURCE_DIR}/bamtools/lib/libbamtools.a ${ZLIB_LIBRARIES})
++include_directories(${bamtools_INCLUDE_DIRS})
+
++set(LIBRARIES ${bamtools_LIBRARY})
+ add_executable(bam-read ${BAMREAD_SRCS} ${BAMREAD_HEADERS})
+
+-set_target_properties(bam-read PROPERTIES LINK_SEARCH_START_STATIC 1)
+-set_target_properties(bam-read PROPERTIES LINK_SEARCH_END_STATIC 1)
+ target_link_libraries(bam-read ${LIBRARIES})
+--- transrate-tools.orig/src/bam-read.h
++++ transrate-tools/src/bam-read.h
+@@ -3,7 +3,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <vector>
+-#include "api/BamReader.h"
++#include "/usr/include/bamtools/api/BamReader.h"
+ #include "pileup.h"
+
+ using namespace BamTools;
+--- transrate-tools.orig/src/pileup.h
++++ transrate-tools/src/pileup.h
+@@ -2,7 +2,7 @@
+ #include <string>
+ #include <vector>
+ #include <math.h>
+-#include "api/BamAlignment.h"
++#include "/usr/include/bamtools/api/BamAlignment.h"
+ #include "segmenter.h"
+
+ extern double nullprior;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..ed522ab
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+cmake-bamtools
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1d11ebc
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/transrate-tools.install b/debian/transrate-tools.install
new file mode 100644
index 0000000..e52cd5d
--- /dev/null
+++ b/debian/transrate-tools.install
@@ -0,0 +1 @@
+./obj-x86_64-linux-gnu/src/bam-read /usr/bin/
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..44e4245
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,15 @@
+version=3
+# Uncomment to find new files on Github
+# - when using releases:
+https://github.com/Blahah/transrate-tools/releases .*/archive/v(\d[\d.-]+)\.(?: tar(?:\.gz|\.bz2)?|tgz)
+# - when using tags
+# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
+# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
+
+# if tweaking of source is needed
+# \
+# debian debian/get-orig-source
+
+# if you need to repack and choose +dfsg prefix
+# opts=dversionmangle=s/[~\+]dfsg[0-9]*// \
+#
--
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