source: branches/0.10-stable/test/Makefile.am @ 2953

Last change on this file since 2953 was 2953, checked in by Peter, 10 years ago

implement BamHeader::target_length(). fixes #740

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 9.5 KB
Line 
1## Process this file with automake to produce Makefile.in
2##
3## $Id: Makefile.am 2953 2013-01-16 07:39:27Z peter $
4
5# Copyright (C) 2003 Daniel Dalevi, Jari Häkkinen
6# Copyright (C) 2004 Jari Häkkinen, Peter Johansson, Cecilia Ritz
7# Copyright (C) 2005 Jari Häkkinen, Peter Johansson
8# Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
9# Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
10#
11# This file is part of the yat library, http://dev.thep.lu.se/yat
12#
13# The yat library is free software; you can redistribute it
14# and/or modify it under the terms of the GNU General Public License as
15# published by the Free Software Foundation; either version 3 of the
16# License, or (at your option) any later version.
17#
18# The yat library is distributed in the hope that it will be useful,
19# but WITHOUT ANY WARRANTY; without even the implied warranty of
20# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
21# General Public License for more details.
22#
23# You should have received a copy of the GNU General Public License
24# along with yat. If not, see <http://www.gnu.org/licenses/>.
25
26## we use suffix .cc for all source
27AM_DEFAULT_SOURCE_EXT = .cc
28
29noinst_HEADERS = test/Suite.h
30
31check_LTLIBRARIES = test/libyattest.la
32
33check_SCRIPTS = test/common_defs.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_pair_analyse test/bam_iterator test/bam_region_iterator \
42  test/bam_header \
43  test/codon.test test/commandline.test \
44  test/concept.test \
45  test/consensus_inputranker.test test/data_lookup_1d.test  \
46  test/data_weight.test test/data_weight_proxy.test \
47  test/deleter.test \
48  test/distance.test \
49  test/dna.test test/ensemble.test test/feature_selection.test \
50  test/fileutil.test \
51  test/fisher.test test/genomic_position.test test/getline_iterator.test \
52  test/gff.test test/help.test test/histogram.test \
53  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
54  test/iterator.test test/kendall.test test/kernel_lookup.test \
55  test/kernel_pca.test test/kernel.test \
56  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
57  test/matrix_lookup.test \
58  test/matrix_lookup_weighted.test test/matrix.test \
59  test/matrix_weighted.test test/merge.test test/nbc.test \
60  test/ncc.test test/nni.test test/normalization.test test/pca.test \
61  test/range.test test/regression.test test/rnd.test \
62  test/rng-mt.test \
63  test/roc.test \
64  test/score.test test/segment.test test/smart_ptr.test   \
65  test/smoother.test test/spearman.test \
66  test/split.test test/statistics.test test/stream_redirect.test \
67  test/subset_generator.test test/svd.test test/svm.test \
68  test/svm_multi_class.test test/target.test \
69  test/ttest.test test/tukey.test \
70  test/utility.test test/vector.test test/version.test test/view.test
71
72TESTS = $(EXTRA_PROGRAMS)
73CLEANFILES += $(EXTRA_PROGRAMS)
74
75# tests not passing through yet
76XFAIL_TESTS =
77
78DISTRIBUTED_TESTS = \
79test/cmd_test.sh \
80test/doxygen_test.sh \
81test/help_test.sh \
82test/static_test.sh \
83test/yat_config_test.sh \
84test/yat_config_cblas_test.sh \
85test/yat_cpp_add_flag_test.sh \
86test/yat_cxx_add_flag_test.sh \
87test/yat_ld_add_flag_test.sh \
88test/yat_have_svn_wc_test.sh \
89test/yat_lt_link_ifelse_test.sh \
90test/yat_msg_error_test.sh \
91test/yat_msg_error_test2.sh \
92test/yat_m4_test.sh \
93test/yat_m4_test2.sh \
94test/yat_prog_move_if_change_test.sh \
95test/yat_revision_header_test.sh \
96test/yat_svn_release_year_test.sh \
97test/yat_svn_revision_test.sh
98
99TESTS += $(DISTRIBUTED_TESTS)
100EXTRA_DIST += $(DISTRIBUTED_TESTS)
101
102TEST_EXTENSIONS = .sh .test
103
104LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
105
106#test_large_file_test_LDADD = test/libyattest.la
107
108test_libyattest_la_LIBADD = yat/libyat.la
109test_libyattest_la_SOURCES = test/Suite.cc
110
111lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
112
113# dependencies for lazycheck
114test/cmd_test.log: test/help.test test/common_defs.sh
115test/help_test.log: test/help.test test/common_defs.sh
116test/static_test.log: $(srcdir)/m4/yat.m4 test/common_defs.sh
117test/yat_config_test.log: build_support/yat-config \
118  build_support/for_installation/yat-config test/common_defs.sh
119test/yat_config_cblas_test.log: build_support/yat-config test/common_defs.sh
120test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
121  $(srcdir)/m4/ax_append_flag.m4 \
122  $(srcdir)/m4/ax_check_preproc_flag.m4 \
123  test/common_defs.sh
124test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
125  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
126  $(top_srcdir)/m4/ax_append_flag.m4 \
127  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
128  test/common_defs.sh
129test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 test/common_defs.sh
130test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
131  $(top_srcdir)/m4/ax_append_flag.m4 \
132  $(top_srcdir)/m4/ax_append_link_flags.m4 \
133  $(top_srcdir)/m4/ax_check_link_flag.m4 \
134  test/common_defs.sh
135test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
136  $(top_srcdir)/m4/yat.m4 test/common_defs.sh \
137  $(top_builddir)/build_support/yat-config
138test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 test/common_defs.sh \
139  $(top_builddir)/build_support/yat-config
140test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 test/common_defs.sh
141test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 test/common_defs.sh
142test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 test/common_defs.sh
143test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
144  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
145  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
146  $(top_srcdir)/m4/ax_file_escapes.m4 \
147  test/common_defs.sh
148test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
149  test/common_defs.sh \
150  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
151  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
152  $(top_srcdir)/m4/ax_file_escapes.m4
153test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
154  test/common_defs.sh \
155  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
156  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
157  $(top_srcdir)/m4/ax_file_escapes.m4
158test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
159  test/common_defs.sh \
160  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
161  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
162  $(top_srcdir)/m4/ax_file_escapes.m4
163
164if DX_ENABLE_HTML
165test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
166endif
167
168# yat-hello is an example of a tiny package that uses yat
169noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
170
171# Directory yat-hello contains what a developer would check out
172# from a VCS, i.e., no files generated by autotools.
173yat_hello_sources  =
174yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
175yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
176yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
177
178EXTRA_DIST += $(yat_hello_sources)
179
180yat_hello_tmp_files =
181yat_hello_tmp_files += Makefile.in
182yat_hello_tmp_files += autom4te.cache
183yat_hello_tmp_files += aclocal.m4
184yat_hello_tmp_files += build-aux
185yat_hello_tmp_files += configure
186yat_hello_tmp_files += m4
187
188
189yat_hello_deps = $(yat_hello_sources)
190yat_hello_deps += $(top_srcdir)/m4/yat.m4
191## We depend on version.m4 so tarball is updated at every release (at least)
192yat_hello_deps += $(top_srcdir)/m4/version.m4
193
194EXTRA_DIST += $(srcdir)/test/yat-hello-1.0.tar.gz
195
196$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
197  $(AM_V_GEN)cd $(srcdir)/test/yat-hello \
198  && $(MKDIR_P) m4 \
199  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
200  && autoreconf -if $(yat_dev_null) \
201  && ./configure --without-yat $(yat_dev_null) \
202  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
203  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
204  && mv yat-hello-1.0.tar.gz .. \
205  && rm -rf $(yat_hello_tmp_files)
206
207INSTALL_CHECK_TARGETS += yat-hello-check
208
209yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
210  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
211  && cd yat-hello-1.0 \
212  && ./configure --with-yat=$(bindir) \
213  && $(MAKE) $(AM_MAKEFLAGS) all \
214  && ./hello \
215  && cd .. \
216  && rm -rf yat-hello-1.0
217
218
219## test data
220EXTRA_DIST += \
221test/data/foo.sam \
222test/data/isoform.peaks \
223test/data/knni_matrix.data \
224test/data/knni_result.data \
225test/data/knni_weight.data \
226test/data/nm_alpha_linear_matlab.txt \
227test/data/nm_data_centralized.txt \
228test/data/nm_kernel.txt \
229test/data/nm_kernel2.txt \
230test/data/nm_kernel_gaussian.txt \
231test/data/nm_target_bin.txt \
232test/data/normalization_test.data \
233test/data/rank_data.txt \
234test/data/rank_target.txt \
235test/data/regression_gauss.data \
236test/data/small.gff2 \
237test/data/small.gff3 \
238test/data/sorlie_centroid_classes.txt \
239test/data/sorlie_centroid_data.txt  \
240test/data/sorlie_centroid_predictions.txt \
241test/data/sorlie_centroids.txt \
242test/data/vector1.data  \
243test/data/vector2.data \
244test/data/vector3.data \
245test/data/vector4.data \
246test/data/vector5.data \
247test/data/vector6.data  \
248test/data/vector7.data \
249test/data/wenni_result.data \
250test/data/wenni_weight.data
251
252CLEANFILES += test/data/.dirstamp
253CLEANFILES += test/data/foo.bam
254CLEANFILES += test/data/foo.sorted.bam
255CLEANFILES += test/data/foo.sorted.bam.bai
256
257check_DATA  = test/data/foo.sorted.bam
258check_DATA += test/data/foo.sorted.bam.bai
259
260test/data/.dirstamp:
261  @$(MKDIR_P) test/data
262  @: > $@
263
264if HAVE_SAMTOOLS
265test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
266  $(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam > $@-t && mv $@-t $@
267
268test/data/foo.sorted.bam: test/data/foo.bam
269  $(SAMTOOLS) sort test/data/foo.bam test/data/foo.sorted
270
271test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
272  $(SAMTOOLS) index test/data/foo.sorted.bam
273else
274test/data/foo.sorted.bam: test/data/.dirstamp
275  : > $@
276
277test/data/foo.sorted.bam.bai: test/data/.dirstamp
278  : > $@
279endif
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