source: branches/0.12-stable/test/Makefile.am @ 3339

Last change on this file since 3339 was 3339, checked in by Peter, 7 years ago

Fix problem that Aligner::member_ is not cleared to 'none' before
aligning, which means that the beginning of alignment could be
incorrect. Fixes #820.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 11.1 KB
Line 
1## $Id: Makefile.am 3339 2014-11-05 23:43:01Z peter $
2
3# Copyright (C) 2003 Daniel Dalevi, Jari Häkkinen
4# Copyright (C) 2004 Jari Häkkinen, Peter Johansson, Cecilia Ritz
5# Copyright (C) 2005 Jari Häkkinen, Peter Johansson
6# Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
7# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014 Peter Johansson
8#
9# This file is part of the yat library, http://dev.thep.lu.se/yat
10#
11# The yat library is free software; you can redistribute it
12# and/or modify it under the terms of the GNU General Public License as
13# published by the Free Software Foundation; either version 3 of the
14# License, or (at your option) any later version.
15#
16# The yat library is distributed in the hope that it will be useful,
17# but WITHOUT ANY WARRANTY; without even the implied warranty of
18# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
19# General Public License for more details.
20#
21# You should have received a copy of the GNU General Public License
22# along with yat. If not, see <http://www.gnu.org/licenses/>.
23
24## we use suffix .cc for all source
25AM_DEFAULT_SOURCE_EXT = .cc
26
27noinst_HEADERS = test/Suite.h
28
29check_LTLIBRARIES = test/libyattest.la
30
31check_SCRIPTS = test/defs.sh
32
33EXTRA_DIST += test/init.sh
34
35EXTRA_PROGRAMS = test/alignment.test \
36  test/alignment2.test \
37  test/averager.test \
38  test/averager1.test \
39  test/averager3.test \
40  test/averager4.test \
41  test/bam.test \
42  test/bam_pair_analyse.test \
43  test/bam_iterator.test \
44  test/bam_read_filter.test \
45  test/bam_region_iterator.test \
46  test/bam_header.test \
47  test/bam_header2.test \
48  test/bam_pair_iterator.test \
49  test/cigar.test \
50  test/cigar2.test \
51  test/codon.test test/commandline.test \
52  test/concept.test \
53  test/consensus_inputranker.test test/data_lookup_1d.test  \
54  test/data_weight.test test/data_weight_proxy.test \
55  test/deleter.test \
56  test/distance.test \
57  test/dna.test test/ensemble.test test/feature_selection.test \
58  test/fileutil.test \
59  test/fisher.test test/genomic_position.test test/getline_iterator.test \
60  test/gff.test test/help.test test/histogram.test \
61  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
62  test/iterator.test test/kendall.test test/kernel_lookup.test \
63  test/kernel_matrix.test \
64  test/kernel_pca.test test/kernel.test \
65  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
66  test/likelihood_ratio_test_binomial.test \
67  test/matrix_lookup.test \
68  test/matrix_lookup_weighted.test test/matrix.test \
69  test/matrix_weighted.test test/merge.test \
70  test/merge_iterator.test test/nbc.test \
71  test/ncc.test test/nni.test test/normalization.test \
72  test/ostream_iterator.test \
73  test/pca.test \
74  test/queue.test test/queue2.test \
75  test/range.test test/regression.test test/rnd.test \
76  test/rng-mt.test \
77  test/roc.test \
78  test/score.test test/segment.test test/smart_ptr.test   \
79  test/smith_waterman.test \
80  test/smoother.test test/spearman.test \
81  test/split.test test/statistics.test test/stream_redirect.test \
82  test/subset_generator.test test/svd.test test/svm.test \
83  test/svm_multi_class.test test/target.test \
84  test/ttest.test test/tukey.test \
85  test/utility.test test/vector.test test/version.test test/view.test
86
87TESTS = $(EXTRA_PROGRAMS)
88CLEANFILES += $(EXTRA_PROGRAMS)
89
90# tests not passing through yet
91XFAIL_TESTS =
92
93DISTRIBUTED_TESTS = \
94test/cmd_test.sh \
95test/doxygen_test.sh \
96test/help_test.sh \
97test/static_test.sh \
98test/yat_config_test.sh \
99test/yat_config_cblas_test.sh \
100test/yat_cpp_add_flag_test.sh \
101test/yat_cxx_add_flag_test.sh \
102test/yat_ld_add_flag_test.sh \
103test/yat_have_svn_wc_test.sh \
104test/yat_lt_compile_ifelse_test.sh \
105test/yat_lt_link_ifelse_test.sh \
106test/yat_lt_link_la_ifelse_test.sh \
107test/yat_msg_error_test.sh \
108test/yat_msg_error_test2.sh \
109test/yat_m4_with_bam_test.sh \
110test/yat_m4_test.sh \
111test/yat_m4_test2.sh \
112test/yat_pc_test.sh \
113test/yat_prog_move_if_change_test.sh \
114test/yat_revision_header_test.sh \
115test/yat_svn_release_year_test.sh \
116test/yat_svn_revision_test.sh \
117test/yat_use_libtool_tag_test.sh
118
119TESTS += $(DISTRIBUTED_TESTS)
120EXTRA_DIST += $(DISTRIBUTED_TESTS)
121
122TEST_EXTENSIONS = .sh .test
123
124LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
125
126#test_large_file_test_LDADD = test/libyattest.la
127
128test_libyattest_la_LIBADD = yat/libyat.la
129test_libyattest_la_SOURCES = test/Suite.cc
130
131lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
132
133shell_test_deps = $(srcdir)/test/init.sh test/defs.sh
134
135# dependencies for lazycheck
136test/cmd_test.log: test/help.test $(shell_test_deps)
137test/help_test.log: test/help.test $(shell_test_deps)
138test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
139test/yat_config_test.log: build_support/yat-config \
140  build_support/for_installation/yat-config $(shell_test_deps)
141test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
142test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
143  $(srcdir)/m4/ax_append_flag.m4 \
144  $(srcdir)/m4/ax_check_preproc_flag.m4 \
145  $(shell_test_deps)
146test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
147  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
148  $(top_srcdir)/m4/ax_append_flag.m4 \
149  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
150  $(shell_test_deps)
151test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
152test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
153  $(top_srcdir)/m4/ax_append_flag.m4 \
154  $(top_srcdir)/m4/ax_append_link_flags.m4 \
155  $(top_srcdir)/m4/ax_check_link_flag.m4 \
156  $(shell_test_deps)
157test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
158  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
159test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
160  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
161  $(top_builddir)/build_support/yat-config
162test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
163  test/lib/libmy-shared.la \
164  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
165  $(top_srcdir)/m4/yat_common.m4
166test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
167  $(top_builddir)/build_support/yat-config
168test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
169test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
170test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
171test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
172test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
173  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
174  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
175  $(top_srcdir)/m4/ax_file_escapes.m4 \
176  $(shell_test_deps)
177test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
178  $(shell_test_deps) \
179  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
180  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
181  $(top_srcdir)/m4/ax_file_escapes.m4
182test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
183  $(shell_test_deps) \
184  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
185  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
186  $(top_srcdir)/m4/ax_file_escapes.m4
187test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
188  $(shell_test_deps) \
189  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
190  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
191  $(top_srcdir)/m4/ax_file_escapes.m4
192test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
193  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
194
195if DX_ENABLE_HTML
196test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
197endif
198
199# yat-hello is an example of a tiny package that uses yat
200dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
201
202# Directory yat-hello contains what a developer would check out
203# from a VCS, i.e., no files generated by autotools.
204yat_hello_sources  =
205yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
206yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
207yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
208
209EXTRA_DIST += $(yat_hello_sources)
210
211yat_hello_tmp_files =
212yat_hello_tmp_files += Makefile.in
213yat_hello_tmp_files += autom4te.cache
214yat_hello_tmp_files += aclocal.m4
215yat_hello_tmp_files += build-aux
216yat_hello_tmp_files += configure
217yat_hello_tmp_files += m4
218
219
220yat_hello_deps = $(yat_hello_sources)
221yat_hello_deps += $(top_srcdir)/m4/yat.m4
222## We depend on version.m4 so tarball is updated at every release (at least)
223yat_hello_deps += $(top_srcdir)/m4/version.m4
224
225$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
226  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
227  && cd $(srcdir)/test/yat-hello \
228  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
229  && autoreconf -if $(yat_dev_null) \
230  && ./configure --without-yat $(yat_dev_null) \
231  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
232  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
233  && mv yat-hello-1.0.tar.gz .. \
234  && rm -rf $(yat_hello_tmp_files)
235
236INSTALL_CHECK_TARGETS += yat-hello-check
237
238yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
239  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
240  && cd yat-hello-1.0 \
241  && ./configure --with-yat=$(bindir) \
242  && $(MAKE) $(AM_MAKEFLAGS) all \
243  && ./hello \
244  && test x"`./hello`" = x"$(VERSION)" \
245  && cd .. \
246  && rm -rf yat-hello-1.0
247
248
249## test data
250EXTRA_DIST += \
251test/data/foo.sam \
252test/data/isoform.peaks \
253test/data/knni_matrix.data \
254test/data/knni_result.data \
255test/data/knni_weight.data \
256test/data/nm_alpha_linear_matlab.txt \
257test/data/nm_data_centralized.txt \
258test/data/nm_kernel.txt \
259test/data/nm_kernel2.txt \
260test/data/nm_kernel_gaussian.txt \
261test/data/nm_target_bin.txt \
262test/data/normalization_test.data \
263test/data/rank_data.txt \
264test/data/rank_target.txt \
265test/data/regression_gauss.data \
266test/data/small.gff2 \
267test/data/small.gff3 \
268test/data/sorlie_centroid_classes.txt \
269test/data/sorlie_centroid_data.txt  \
270test/data/sorlie_centroid_predictions.txt \
271test/data/sorlie_centroids.txt \
272test/data/vector1.data  \
273test/data/vector2.data \
274test/data/vector3.data \
275test/data/vector4.data \
276test/data/vector5.data \
277test/data/vector6.data  \
278test/data/vector7.data \
279test/data/wenni_result.data \
280test/data/wenni_weight.data
281
282CLEANFILES += test/data/.dirstamp
283CLEANFILES += test/data/foo.bam
284CLEANFILES += test/data/foo.sorted.bam
285CLEANFILES += test/data/foo.sorted.bam.bai
286
287check_DATA  = test/data/foo.sorted.bam
288check_DATA += test/data/foo.sorted.bam.bai
289
290test/data/.dirstamp:
291  @$(MKDIR_P) test/data
292  @: > $@
293
294if HAVE_SAMTOOLS
295test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
296  $(AM_V_GEN)
297  $(AM_V_at)$(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam \
298  > $@-t && mv $@-t $@
299
300test/data/foo.sorted.bam: test/data/foo.bam
301  $(AM_V_GEN)
302  $(AM_V_at)$(SAMTOOLS) sort test/data/foo.bam test/data/foo.sorted
303
304test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
305  $(AM_V_GEN)
306  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
307else
308test/data/foo.sorted.bam: test/data/.dirstamp
309  $(AM_V_at): > $@
310
311test/data/foo.sorted.bam.bai: test/data/.dirstamp
312  $(AM_V_at): > $@
313endif
314
315test/lib/.dirstamp:
316  @$(MKDIR_P) test/lib
317  @: > $@
318
319check_DATA += test/lib/libmy-static.a
320EXTRA_DIST += test/gen_libmy_static.sh
321
322test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
323test/defs.sh
324  $(AM_V_GEN)
325  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)
326
327check_DATA += test/lib/libmy-shared.la
328EXTRA_DIST += test/gen_libmy_shared.sh
329
330test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
331test/defs.sh
332  $(AM_V_GEN)
333  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)
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