[med-svn] [fsm-lite] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Fri Apr 8 19:18:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fsm-lite.
commit eb86cd51a560211d503682092bad19bb7a90c725
Author: Andreas Tille <tille at debian.org>
Date: Fri Apr 8 21:17:42 2016 +0200
Initial packaging
---
debian/README.Debian | 2 +
debian/changelog | 5 +
debian/clean | 1 +
debian/compat | 1 +
debian/control | 20 ++++
debian/copyright | 11 ++
debian/get-orig-source | 24 ++++
debian/install | 1 +
debian/patches/series | 1 +
debian/patches/use_debian_packaged_libsdsl.patch | 133 +++++++++++++++++++++++
debian/rules | 9 ++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++
debian/watch | 1 +
14 files changed, 222 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..e7987ed
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,2 @@
+May be the tool dfi from seqan-apps package fits the same purpose.
+ see https://www.seqan.de/projects/dfi/
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ab21400
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+fsm-lite (0.0+20151109-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Apr 2016 10:01:02 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..bcd672a
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+tmp.*
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..c999fd9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,20 @@
+Source: fsm-lite
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libsdsl-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fsm-lite.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/fsm-lite.git
+Homepage: https://github.com/nvalimak/fsm-lite
+
+Package: fsm-lite
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: frequency-based string mining (lite)
+ A singe-core implementation of frequency-based substring mining used in
+ ioinformatics to extract substrings that discriminate two (or more)
+ datasets inside high-throughput sequencing data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8394b19
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: fsm-lite
+Source: https://github.com/nvalimak/fsm-lite
+
+Files: *
+Copyright: 2015 Niko Välimäki
+License: to_be_clarified
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-3+
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..a115319
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,24 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+git clone --quiet https://github.com/nvalimak/${NAME}.git
+cd ${NAME}
+VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
+# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
+git restore-mtime || true
+cd ..
+TARDIR=${NAME}-${VERSION}
+mv ${NAME} ${TARDIR}
+rm -rf ${TARDIR}/.git
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..f120c3b
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+fsm-lite usr/bin
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c160ee0
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_libsdsl.patch
diff --git a/debian/patches/use_debian_packaged_libsdsl.patch b/debian/patches/use_debian_packaged_libsdsl.patch
new file mode 100644
index 0000000..4e01d48
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libsdsl.patch
@@ -0,0 +1,133 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 08 Apr 2016 10:01:02 +0200
+Description: Upstream hardcodes local path to libsdsl which is removed here
+
+--- a/dependencies.mk
++++ b/dependencies.mk
+@@ -1,99 +1,3 @@
+ configuration.o: configuration.cpp configuration.h input_reader.h
+-fsm-lite.o: fsm-lite.cpp default.h configuration.h input_reader.h \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_trees.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/sdsl_concepts.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/uintx_t.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_arrays.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/csa_bitcompressed.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/int_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bits.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/structure_tree.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/config.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/util.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/sfstream.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/ram_fs.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/ram_filebuf.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/io.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/memory_management.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/int_vector_buffer.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/iterators.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_array_helper.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/csa_sampling_strategy.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/csa_alphabet_strategy.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/sd_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/select_support_mcl.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/select_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rank_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rank_support_v.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rank_support_v5.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rank_support_scan.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/select_support_scan.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/csa_wt.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wavelet_trees.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_pc.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bit_vectors.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bit_vector_il.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rrr_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rrr_helper.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/uint128_t.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/uint256_t.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rrr_vector_15.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_helper.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_blcd.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_gmr.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/vectors.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/enc_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/coder.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/coder_fibonacci.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/coder_elias_delta.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/coder_elias_gamma.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/coder_comma.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/vlc_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/dac_vector.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_huff.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_hutu.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_int.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wm_int.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_rlmn.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_lcp.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_isa.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_bwt.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/wt_algorithm.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_lcp_helper.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_sa.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/divsufsort.h \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/divsufsort64.h \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/qsufsort.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_sa_se.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/construct_config.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/fast_cache.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/csa_sada.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_array_algorithm.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_tree_algorithm.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/suffix_tree_helper.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/sorted_multi_stack_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/sorted_stack_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/cst_sct3.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_support_sada.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_byte.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_wt.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_vlc.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_dac.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_bitcompressed.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_support_tree.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/lcp_support_tree2.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bp_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bp_support_g.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/nearest_neighbour_dictionary.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rmq_support.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rmq_support_sparse_table.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rmq_succinct_sct.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bp_support_sada.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bp_support_algorithm.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/rmq_succinct_sada.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/bp_support_gg.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/cst_iterators.hpp \
+- /Users/nvalimak/code/sdsl-lite-2.0.3/include/sdsl/cst_sada.hpp
++fsm-lite.o: fsm-lite.cpp default.h configuration.h input_reader.h
+ input_reader.o: input_reader.cpp default.h input_reader.h configuration.h
+--- a/Makefile
++++ b/Makefile
+@@ -1,13 +1,11 @@
+-SDSL_INSTALL_PREFIX=/Users/nvalimak/code/sdsl-lite-2.0.3
+-
+ CC=g++
+-CPPFLAGS=-std=c++11 -I${SDSL_INSTALL_PREFIX}/include
++CPPFLAGS+=-std=c++11
+ DISBALEDOPTIMIZATIONFLAGS = -DNDEBUG -O3 -msse4.2
+ LIBS=-lsdsl -ldivsufsort -ldivsufsort64
+ OBJ = configuration.o input_reader.o
+
+ fsm-lite: fsm-lite.o $(OBJ)
+- $(CC) $(CPPFLAGS) -L${SDSL_INSTALL_PREFIX}/lib -o fsm-lite fsm-lite.o $(OBJ) $(LIBS)
++ $(CC) $(CPPFLAGS) -o fsm-lite fsm-lite.o $(OBJ) $(LIBS) $(LDFLAGS)
+
+ test: fsm-lite
+ ./fsm-lite -l test.list -t tmp -v --debug -m 1
+@@ -16,6 +14,6 @@ clean:
+ rm -f fsm-lite *.o *~
+
+ depend:
+- g++ -MM -std=c++11 -I${SDSL_INSTALL_PREFIX}/include *.cpp > dependencies.mk
++ g++ -MM -std=c++11 *.cpp > dependencies.mk
+
+ include dependencies.mk
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..45a64ae
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+override_dh_auto_test:
+ echo "Upstream source is lacking file test.list which is needed for testing."
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/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..0fc4a5a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1 @@
+# Upstream does not tag releases
--
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