[med-svn] [Git][med-team/isovic-seqlib][master] Attempt to create library using automake

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / isovic-seqlib


Commits:
20965564 by Andreas Tille at 2021-11-23T11:00:26+01:00
Attempt to create library using automake

- - - - -


2 changed files:

- + debian/patches/autoconf.patch
- + debian/patches/series


Changes:

=====================================
debian/patches/autoconf.patch
=====================================
@@ -0,0 +1,110 @@
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,3 @@
++SUBDIRS = sample-data src test_src
++
++EXTRA_DIST = EXTRA_DIST README.md
+--- /dev/null
++++ b/sample-data/Makefile.am
+@@ -0,0 +1 @@
++EXTRA_DIST = test.fastq  test.gfa  test.sam
+--- /dev/null
++++ b/src/Makefile.am
+@@ -0,0 +1,25 @@
++lib_LTLIBRARIES  = libisovic_seqlib.la
++
++libisovic_seqlibdir=$(includedir)/isovic-seqlib
++libisovic_seqlib_HEADERS= sequences/sequence_alignment.h sequences/sequence_file.h sequences/sequence_gfa.h sequences/single_sequence.h \
++                          utility/tictoc.h utility/utility_general.h
++libisovic_seqlib_la_SOURCES = algorithm/fenwick.h algorithm/lis.hpp \
++                              libs/edlib.cc libs/edlibcigar.cc libs/edlibcigar.h libs/edlib.h libs/opal.cc libs/opal.h \
++                              log_system/log_system.cc log_system/log_system.h \
++                              sequences/kseq.h sequences/sequence_alignment.cc \
++                              sequences/sequence_alignment_test.cc sequences/sequence_file.cc \
++                              sequences/sequence_gfa.cc sequences/sequence_gfa_test.cc \
++                              sequences/sequence_test.h sequences/single_sequence.cc \
++                              utility/evalue.cc utility/evalue_constants.cc utility/evalue_constants.h utility/evalue.h \
++                              utility/tictoc.cc utility/utility_conversion-inl.h utility/utility_general.cc
++libisovic_seqlib_la_LDFLAGS = -version-info @LIB_VERSION@
++
++libisovic_seqlib_la_CPPFLAGS = $(INCLUDES)
++
++#bin_PROGRAMS = test
++#isovic_seqlib_SOURCES = test.cc
++#isovic_seqlib_LDADD = libisovic_seqlib.la -ldivsufsort -lseqan2
++
++#pkgconfigdir=$(libdir)/pkgconfig
++#pkgconfig_DATA = libisovic_seqlib.pc
++
+--- /dev/null
++++ b/test_src/Makefile.am
+@@ -0,0 +1,3 @@
++noinst_PROGRAMS = test_lis
++test_lis_SOURCES = test_lis.cc
++LDADD           = $(top_builddir)/src/libisovic_seqlib.la
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,63 @@
++#                                               -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_INIT(isovic-seqlib, 0.0, Ivan Sovic)
++AC_CONFIG_HEADERS([config.h])
++
++AC_PREREQ(2.57)
++
++#	Directory that contains install-sh and other auxiliary files
++AC_CONFIG_AUX_DIR([config])
++
++################################################################################
++#	According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)
++#		this macro should be after AC_INIT but before AM_INIT_AUTOMAKE
++################################################################################
++AC_CONFIG_MACRO_DIR(config)
++
++AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
++
++LIB_VERSION=0:0
++
++AC_SUBST([VERSION])
++AC_SUBST([LIB_VERSION])
++
++AC_SUBST([VERSION])
++
++# Checks for programs.
++AC_PROG_LN_S
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++
++################################################################################
++# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
++#	the AX_CXXFLAGS macro below.
++# So we cache the argument to configure
++#	here in ARG_CXX_FLAGS (so that our macro does not override them)
++################################################################################
++ARG_CXX_FLAGS="$CXXFLAGS"
++AC_PROG_CXX
++
++#Ranlib handled by check for libtool
++CXXFLAGS="$ARG_CXX_FLAGS"
++AX_CXXFLAGS
++
++AC_SUBST(CXXFLAGS)
++
++CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"
++# Checks for libraries.
++
++# Checks for header files.
++AC_HEADER_STDC
++AC_CHECK_HEADERS([stdlib.h])
++
++AC_PROG_MAKE_SET
++
++AC_CONFIG_FILES([
++	Makefile
++        sample-data/Makefile
++        src/Makefile
++        test_src/Makefile
++	])
++AC_OUTPUT
++


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+autoconf.patch



View it on GitLab: https://salsa.debian.org/med-team/isovic-seqlib/-/commit/209655648bbebe319cbbdd095592f44a4d5c9292

-- 
View it on GitLab: https://salsa.debian.org/med-team/isovic-seqlib/-/commit/209655648bbebe319cbbdd095592f44a4d5c9292
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