Merge branch 'master' (changes made for V2.0.8) into develop

Conflicts:
	README.md
	configure.ac
	scripts/.gitignore

Makefile.am

@@ -2,29 +2,12 @@
 # Tells aclocal to put 'aclocal.m4' into the 'm4' directory
 ACLOCAL_AMFLAGS = -I m4 ${ACLOCAL_FLAGS}
 
-SEQAN_ARCHIVE = deps/seqan-library-2.0.0.tar.gz
-
-dist_pkgdata_DATA = $(SEQAN_ARCHIVE)
-
-install-data-hook:
-	cd $(DESTDIR)/deps; \
-	cat $(SEQAN_ARCHIVE) | gunzip | $(TAR) -H gnu --list > uninstall_manifest.txt; \
-	cat $(SEQAN_ARCHIVE) | gunzip | $(TAR) -H gnu --no-same-owner --extract; \
-	rm --force $(SEQAN_ARCHIVE); \
-	cat uninstall_manifest.txt | sed --expression='s/^\|$$/"/g' | xargs chmod a=rX,u+w
-
-uninstall-local:
-	cd $(DESTDIR)/deps; \
-	cat uninstall_manifest.txt | sed --expression='s/ /\\ /g' | xargs rm --force; \
-	rm --force uninstall_manifest.txt
-
 # ADDITIONAL FILES TO INSTALL
 EXTRA_DIST =	README.md \
 		COPYING \
 		AUTHORS \
 		INSTALL \
-		ChangeLog \
-		deps/seqan-library-2.0.0
+		ChangeLog
 
 
 # Scripts NOT to install
@@ -42,6 +25,6 @@ dist_bin_SCRIPTS =	scripts/dist_analysis.py \
 			scripts/spectra-mx.py
 
 # SRC DIRS
-SUBDIRS = deps/jellyfish-2.2.0 src tests
+SUBDIRS = deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 src tests
 
 AUTOMAKE_OPTIONS = subdir-objects

README.md

@@ -27,16 +27,20 @@ Generic installation description can be found in the INSTALL file. Short summary
   - Acquire the source code.  Either download and decompress the distributable ("tar -xvf kat-<version>.tar.gz"), or clone the git repository (For ssh: ```git clone [email protected]:TGAC/KAT.git```; or for https: ```git clone https://github.com/TGAC/KAT.git```), into a directory on your machine.
   - "cd" into root directory of the installation
   - Ensure these tools are correctly installed and available on your system:
-      - gcc tool chain
+      - gcc V4.9+
+      - autoconf V2.53+
+      - automake V1.11+
+      - libtool V2.4.2+
       - make
-
+      - boost V1.53+
+      - Optionally python3 with matplotlib or gnuplot (required for plotting at runtime, must be available on the path to use this functionality)
   - If you cloned the git repository you must first run "./autogen.sh" to create the configure and make files for your project.  (If you downloaded a source code distribution tarball then you can skip this step.)
   - For a typical installation on a machine where you have root access type ```./configure; make; sudo make install;```
 
 
 The configure script can take several options as arguments.  One commonly modified option is ```--prefix```, which will install KAT to a custom directory.  By default this is "/usr/local", so the KAT executable would be found at "/usr/local/bin" by default.  In addition, some options specific to managing KAT dependencies located in non-standard locations are:
 
-  - ```--with-boost``` - for specifying a custom boost directory (boost is only required for unit testing)
+  - ```--with-boost``` - for specifying a custom boost directory
 
 Type ```./configure --help``` for full details.
 

configure.ac

@@ -139,7 +139,7 @@ AC_SUBST([AM_CPPFLAGS])
 AC_SUBST([AM_LIBS])
 
 AC_CONFIG_HEADERS([config.h])
-AC_CONFIG_FILES([Makefile src/Makefile tests/Makefile])
+AC_CONFIG_FILES([Makefile src/Makefile tests/Makefile deps/seqan-library-2.0.0/Makefile])
 AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
 AC_OUTPUT
 

deps/.gitignore

@@ -0,0 +1 @@
+*.txt

deps/jellyfish-2.2.0/Makefile.am

@@ -5,7 +5,7 @@ EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE # jellyfish.spec
 man1_MANS = doc/jellyfish.man
 
 pkgconfigdir = $(libdir)/pkgconfig
-pkgconfig_DATA = jellyfish-2.0.pc
+pkgconfig_DATA = jellyfish-k2.0.pc
 
 AM_LDFLAGS = -lpthread # $(VALGRIND_LIBS)
 AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(top_srcdir) -I$(top_srcdir)/include -g -O3 $(VALGRIND_CFLAGS)
@@ -29,15 +29,15 @@ V_YAGGO_0 = @echo "  YAGGO   " $@;
 YAGGO_SOURCES = # Append all file to be built by yaggo
 
 # What to build
-bin_PROGRAMS += bin/jellyfish
-lib_LTLIBRARIES = libjellyfish-2.0.la
-LDADD = libjellyfish-2.0.la # $(VALGRIND_LIBS)
+bin_PROGRAMS += bin/jellyfishk
+lib_LTLIBRARIES = libjellyfish-k2.0.la
+LDADD = libjellyfish-k2.0.la # $(VALGRIND_LIBS)
 check_PROGRAMS = bin/generate_sequence
 
 ############################
 # Build Jellyfish the exec #
 ############################
-bin_jellyfish_SOURCES = sub_commands/jellyfish.cc	\
+bin_jellyfishk_SOURCES = sub_commands/jellyfish.cc	\
                         sub_commands/count_main.cc	\
                         sub_commands/info_main.cc	\
                         sub_commands/dump_main.cc	\
@@ -49,7 +49,7 @@ bin_jellyfish_SOURCES = sub_commands/jellyfish.cc	\
                         sub_commands/cite_main.cc	\
                         sub_commands/mem_main.cc	\
                         jellyfish/merge_files.cc
-bin_jellyfish_LDFLAGS = $(AM_LDFLAGS) $(STATIC_FLAGS)
+bin_jellyfishk_LDFLAGS = $(AM_LDFLAGS) $(STATIC_FLAGS)
 
 
 YAGGO_SOURCES += sub_commands/count_main_cmdline.hpp	\
@@ -66,8 +66,8 @@ YAGGO_SOURCES += sub_commands/count_main_cmdline.hpp	\
 ######################################
 # Build Jellyfish the shared library #
 ######################################
-libjellyfish_2_0_la_LDFLAGS = -version-info 2:0:0
-libjellyfish_2_0_la_SOURCES = lib/rectangular_binary_matrix.cc		\
+libjellyfish_k2_0_la_LDFLAGS = -version-info 2:0:0
+libjellyfish_k2_0_la_SOURCES = lib/rectangular_binary_matrix.cc		\
                               lib/mer_dna.cc lib/storage.cc		\
                               lib/allocators_mmap.cc lib/misc.cc	\
                               lib/int128.cc lib/thread_exec.cc		\
@@ -140,9 +140,9 @@ SH_LOG_COMPILER = /bin/sh
 AM_SH_LOG_FLAGS =
 
 TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh	\
-        tests/merge.sh tests/bloom_filter.sh tests/big.sh	\
+        tests/merge.sh tests/big.sh	\
         tests/subset_hashing.sh tests/multi_file.sh		\
-        tests/bloom_counter.sh tests/large_key.sh
+        tests/large_key.sh
 
 EXTRA_DIST += $(TESTS)
 clean-local: clean-local-check
@@ -152,22 +152,22 @@ clean-local-check:
 
 tests/parallel_hashing.log: tests/generate_sequence.log
 tests/subset_hashing.log: tests/generate_sequence.log
-tests/bloom_filter.log: tests/generate_sequence.log
-tests/bloom_counter.log: tests/generate_sequence.log
+#tests/bloom_filter.log: tests/generate_sequence.log
+#tests/bloom_counter.log: tests/generate_sequence.log
 tests/multi_file.log: tests/generate_sequence.log
 tests/merge.log: tests/generate_sequence.log
 tests/min_qual.log: tests/generate_fastq_sequence.log
 tests/large_key.log: tests/generate_sequence.log
 tests/quality_filter.log: tests/generate_sequence.log
 
 # SWIG tests
-TESTS += tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh
-tests/swig_python.log: tests/generate_sequence.log
-tests/swig_ruby.log: tests/generate_sequence.log
-tests/swig_perl.log: tests/generate_sequence.log
-EXTRA_DIST += swig/python/test_mer_file.py swig/python/test_hash_counter.py
-EXTRA_DIST += swig/ruby/test_mer_file.rb swig/ruby/test_hash_counter.rb
-EXTRA_DIST += swig/perl5/t/test_mer_file.t swig/perl5/t/test_hash_counter.t
+#TESTS += tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh
+#tests/swig_python.log: tests/generate_sequence.log
+#tests/swig_ruby.log: tests/generate_sequence.log
+#tests/swig_perl.log: tests/generate_sequence.log
+#EXTRA_DIST += swig/python/test_mer_file.py swig/python/test_hash_counter.py
+#EXTRA_DIST += swig/ruby/test_mer_file.rb swig/ruby/test_hash_counter.rb
+#EXTRA_DIST += swig/perl5/t/test_mer_file.t swig/perl5/t/test_hash_counter.t
 
 
 ##############

deps/jellyfish-2.2.0/configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([jellyfish], [2.2.0], [[email protected]])
+AC_INIT([jellyfish], [k2.2.0], [[email protected]])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])
@@ -14,7 +14,7 @@ AC_LANG(C++)
 AC_PROG_CXX
 
 # Major version of the library
-AC_SUBST([PACKAGE_LIB], [2.0])
+AC_SUBST([PACKAGE_LIB], [k2.0])
 
 # Check for md5 or md5sum
 AC_ARG_VAR([MD5], [Path to md5 hashing program])
@@ -27,7 +27,7 @@ AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])
 AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])])
 
 dnl define([concat], $1$2$3)dnl
-define([PC_FILE], jellyfish-2.0.pc)
+define([PC_FILE], jellyfish-k2.0.pc)
 AC_CONFIG_FILES([
     Makefile
     tests/compat.sh

deps/jellyfish-2.2.0/jellyfish-2.0.pc.in → deps/jellyfish-2.2.0/jellyfish-k2.0.pc.in

@@ -6,5 +6,5 @@ includedir=@includedir@
 Name: Jellyfish
 Description: A multi-threaded hash based k-mer counter.
 Version: @PACKAGE_VERSION@
-Libs: -L${libdir} -ljellyfish-2.0 -lpthread
+Libs: -L${libdir} -ljellyfish-k2.0 -lpthread
 Cflags: -I${includedir}/jellyfish-@PACKAGE_VERSION@

deps/seqan-library-2.0.0/.gitignore

@@ -0,0 +1 @@
+/Makefile