source: trunk/test/Makefile.am @ 3173

Last change on this file since 3173 was 3173, checked in by Peter, 8 years ago

a first version of BamPairIterator?. refs #784

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 11.0 KB
Line 
1## $Id: Makefile.am 3173 2014-03-08 13:48:13Z 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/codon.test test/commandline.test \
50  test/concept.test \
51  test/consensus_inputranker.test test/data_lookup_1d.test  \
52  test/data_weight.test test/data_weight_proxy.test \
53  test/deleter.test \
54  test/distance.test \
55  test/dna.test test/ensemble.test test/feature_selection.test \
56  test/fileutil.test \
57  test/fisher.test test/genomic_position.test test/getline_iterator.test \
58  test/gff.test test/help.test test/histogram.test \
59  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
60  test/iterator.test test/kendall.test test/kernel_lookup.test \
61  test/kernel_pca.test test/kernel.test \
62  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
63  test/likelihood_ratio_test_binomial.test \
64  test/matrix_lookup.test \
65  test/matrix_lookup_weighted.test test/matrix.test \
66  test/matrix_weighted.test test/merge.test \
67  test/merge_iterator.test test/nbc.test \
68  test/ncc.test test/nni.test test/normalization.test \
69  test/ostream_iterator.test \
70  test/pca.test \
71  test/queue.test test/queue2.test \
72  test/range.test test/regression.test test/rnd.test \
73  test/rng-mt.test \
74  test/roc.test \
75  test/score.test test/segment.test test/smart_ptr.test   \
76  test/smoother.test test/spearman.test \
77  test/split.test test/statistics.test test/stream_redirect.test \
78  test/subset_generator.test test/svd.test test/svm.test \
79  test/svm_multi_class.test test/target.test \
80  test/ttest.test test/tukey.test \
81  test/utility.test test/vector.test test/version.test test/view.test
82
83TESTS = $(EXTRA_PROGRAMS)
84CLEANFILES += $(EXTRA_PROGRAMS)
85
86# tests not passing through yet
87XFAIL_TESTS =
88
89DISTRIBUTED_TESTS = \
90test/cmd_test.sh \
91test/doxygen_test.sh \
92test/help_test.sh \
93test/static_test.sh \
94test/yat_config_test.sh \
95test/yat_config_cblas_test.sh \
96test/yat_cpp_add_flag_test.sh \
97test/yat_cxx_add_flag_test.sh \
98test/yat_ld_add_flag_test.sh \
99test/yat_have_svn_wc_test.sh \
100test/yat_lt_compile_ifelse_test.sh \
101test/yat_lt_link_ifelse_test.sh \
102test/yat_lt_link_la_ifelse_test.sh \
103test/yat_msg_error_test.sh \
104test/yat_msg_error_test2.sh \
105test/yat_m4_with_bam_test.sh \
106test/yat_m4_test.sh \
107test/yat_m4_test2.sh \
108test/yat_pc_test.sh \
109test/yat_prog_move_if_change_test.sh \
110test/yat_revision_header_test.sh \
111test/yat_svn_release_year_test.sh \
112test/yat_svn_revision_test.sh \
113test/yat_use_libtool_tag_test.sh
114
115TESTS += $(DISTRIBUTED_TESTS)
116EXTRA_DIST += $(DISTRIBUTED_TESTS)
117
118TEST_EXTENSIONS = .sh .test
119
120LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
121
122#test_large_file_test_LDADD = test/libyattest.la
123
124test_libyattest_la_LIBADD = yat/libyat.la
125test_libyattest_la_SOURCES = test/Suite.cc
126
127lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
128
129shell_test_deps = $(srcdir)/test/init.sh test/defs.sh
130
131# dependencies for lazycheck
132test/cmd_test.log: test/help.test $(shell_test_deps)
133test/help_test.log: test/help.test $(shell_test_deps)
134test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
135test/yat_config_test.log: build_support/yat-config \
136  build_support/for_installation/yat-config $(shell_test_deps)
137test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
138test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
139  $(srcdir)/m4/ax_append_flag.m4 \
140  $(srcdir)/m4/ax_check_preproc_flag.m4 \
141  $(shell_test_deps)
142test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
143  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
144  $(top_srcdir)/m4/ax_append_flag.m4 \
145  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
146  $(shell_test_deps)
147test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
148test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
149  $(top_srcdir)/m4/ax_append_flag.m4 \
150  $(top_srcdir)/m4/ax_append_link_flags.m4 \
151  $(top_srcdir)/m4/ax_check_link_flag.m4 \
152  $(shell_test_deps)
153test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
154  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
155test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
156  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
157  $(top_builddir)/build_support/yat-config
158test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
159  test/lib/libmy-shared.la \
160  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
161  $(top_srcdir)/m4/yat_common.m4
162test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
163  $(top_builddir)/build_support/yat-config
164test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
165test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
166test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
167test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
168test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
169  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
170  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
171  $(top_srcdir)/m4/ax_file_escapes.m4 \
172  $(shell_test_deps)
173test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
174  $(shell_test_deps) \
175  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
176  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
177  $(top_srcdir)/m4/ax_file_escapes.m4
178test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
179  $(shell_test_deps) \
180  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
181  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
182  $(top_srcdir)/m4/ax_file_escapes.m4
183test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
184  $(shell_test_deps) \
185  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
186  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
187  $(top_srcdir)/m4/ax_file_escapes.m4
188test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
189  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
190
191if DX_ENABLE_HTML
192test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
193endif
194
195# yat-hello is an example of a tiny package that uses yat
196dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
197
198# Directory yat-hello contains what a developer would check out
199# from a VCS, i.e., no files generated by autotools.
200yat_hello_sources  =
201yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
202yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
203yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
204
205EXTRA_DIST += $(yat_hello_sources)
206
207yat_hello_tmp_files =
208yat_hello_tmp_files += Makefile.in
209yat_hello_tmp_files += autom4te.cache
210yat_hello_tmp_files += aclocal.m4
211yat_hello_tmp_files += build-aux
212yat_hello_tmp_files += configure
213yat_hello_tmp_files += m4
214
215
216yat_hello_deps = $(yat_hello_sources)
217yat_hello_deps += $(top_srcdir)/m4/yat.m4
218## We depend on version.m4 so tarball is updated at every release (at least)
219yat_hello_deps += $(top_srcdir)/m4/version.m4
220
221$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
222  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
223  && cd $(srcdir)/test/yat-hello \
224  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
225  && autoreconf -if $(yat_dev_null) \
226  && ./configure --without-yat $(yat_dev_null) \
227  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
228  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
229  && mv yat-hello-1.0.tar.gz .. \
230  && rm -rf $(yat_hello_tmp_files)
231
232INSTALL_CHECK_TARGETS += yat-hello-check
233
234yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
235  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
236  && cd yat-hello-1.0 \
237  && ./configure --with-yat=$(bindir) \
238  && $(MAKE) $(AM_MAKEFLAGS) all \
239  && ./hello \
240  && test x"`./hello`" = x"$(VERSION)" \
241  && cd .. \
242  && rm -rf yat-hello-1.0
243
244
245## test data
246EXTRA_DIST += \
247test/data/foo.sam \
248test/data/isoform.peaks \
249test/data/knni_matrix.data \
250test/data/knni_result.data \
251test/data/knni_weight.data \
252test/data/nm_alpha_linear_matlab.txt \
253test/data/nm_data_centralized.txt \
254test/data/nm_kernel.txt \
255test/data/nm_kernel2.txt \
256test/data/nm_kernel_gaussian.txt \
257test/data/nm_target_bin.txt \
258test/data/normalization_test.data \
259test/data/rank_data.txt \
260test/data/rank_target.txt \
261test/data/regression_gauss.data \
262test/data/small.gff2 \
263test/data/small.gff3 \
264test/data/sorlie_centroid_classes.txt \
265test/data/sorlie_centroid_data.txt  \
266test/data/sorlie_centroid_predictions.txt \
267test/data/sorlie_centroids.txt \
268test/data/vector1.data  \
269test/data/vector2.data \
270test/data/vector3.data \
271test/data/vector4.data \
272test/data/vector5.data \
273test/data/vector6.data  \
274test/data/vector7.data \
275test/data/wenni_result.data \
276test/data/wenni_weight.data
277
278CLEANFILES += test/data/.dirstamp
279CLEANFILES += test/data/foo.bam
280CLEANFILES += test/data/foo.sorted.bam
281CLEANFILES += test/data/foo.sorted.bam.bai
282
283check_DATA  = test/data/foo.sorted.bam
284check_DATA += test/data/foo.sorted.bam.bai
285
286test/data/.dirstamp:
287  @$(MKDIR_P) test/data
288  @: > $@
289
290if HAVE_SAMTOOLS
291test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
292  $(AM_V_GEN)
293  $(AM_V_at)$(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam \
294  > $@-t && mv $@-t $@
295
296test/data/foo.sorted.bam: test/data/foo.bam
297  $(AM_V_GEN)
298  $(AM_V_at)$(SAMTOOLS) sort test/data/foo.bam test/data/foo.sorted
299
300test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
301  $(AM_V_GEN)
302  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
303else
304test/data/foo.sorted.bam: test/data/.dirstamp
305  $(AM_V_at): > $@
306
307test/data/foo.sorted.bam.bai: test/data/.dirstamp
308  $(AM_V_at): > $@
309endif
310
311test/lib/.dirstamp:
312  @$(MKDIR_P) test/lib
313  @: > $@
314
315check_DATA += test/lib/libmy-static.a
316EXTRA_DIST += test/gen_libmy_static.sh
317
318test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
319test/defs.sh
320  $(AM_V_GEN)
321  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)
322
323check_DATA += test/lib/libmy-shared.la
324EXTRA_DIST += test/gen_libmy_shared.sh
325
326test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
327test/defs.sh
328  $(AM_V_GEN)
329  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)
Note: See TracBrowser for help on using the repository browser.