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Makefile.am
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Makefile.am
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###
##
## AUTHORS
##
## Jeffrey E. Barrick <[email protected]>
## David B. Knoester
##
## LICENSE AND COPYRIGHT
##
## Copyright (c) 2010 Michigan State University
##
## breseq is free software; you can redistribute it and/or modify it under the terms the
## GNU General Public License as published by the Free Software Foundation; either
## version 1, or (at your option) any later version.
##
###
ACLOCAL_AMFLAGS = -I aux_build/m4
SUBDIRS = $(LIBBAM) $(BRESEQ)
### Tests! -- only one test included for now in distribution.
## Top level files included (and required) by default
## AUTHORS, ChangeLog, COPYING, INSTALL, NEWS, README
EXTRA_DIST = \
DEVELOPER \
dev-environment.yml \
run-environment.yml \
tests/common.sh \
tests/test.sh \
tests/lambda_mult_ref_read/expected.gd \
tests/lambda_mult_ref_read/testcmd.sh \
tests/data/lambda/empty.fastq \
tests/data/lambda/only_bad.fastq \
tests/data/lambda/lambda_mixed_population.1.fastq \
tests/data/lambda/lambda_mixed_population.2.fastq \
tests/data/lambda/lambda_mixed_population.3.fastq \
tests/data/lambda/lambda_mixed_population.4.fastq \
tests/data/lambda/lambda_mixed_population.5.fastq \
tests/data/lambda/lambda.1-2.gbk \
tests/data/lambda/lambda.3.gbk \
tests/data/lambda/lambda.4.gbk \
tests/data/lambda/lambda.5.gbk
DOCSRCDIR=$(top_srcdir)/src/doc
DOCBUILDDIR=$(abs_top_builddir)/src/doc/_build
SAMTOOLSDIR=$(top_srcdir)/$(LIBBAM)
## Main hooks called after normal make steps
all-local :
install-exec-local :
clean-local :: clean-tests
## This saves the install path for the test script
rm -f $(abs_top_builddir)/tests/test.config
rm -rf $(DOCBUILDDIR);
find $(abs_top_builddir) -name '.DS_Store' -type f -delete
rm -rf $(abs_top_builddir)/src/c/breseq/*.dSYM
docs :
## This environmental variable is used by python Sphinx
echo $(PACKAGE_VERSION); \
export BRESEQ_VERSION=$(PACKAGE_VERSION); \
cd $(DOCSRCDIR) ; \
make -f Makefile BUILDDIR=$(DOCBUILDDIR) html ;
dist-hook:
if [ -d "$(DOCSRCDIR)" ]; then \
make docs ; \
cp -r $(DOCBUILDDIR)/html $(distdir)/documentation ; \
fi ;
find $(distdir) -name '.DS_Store' -type f -delete
## Remove ._ files
rm -rf `find $(distdir) -name ".*"`
rm -rf ./src/c/breseq/gdtools.dSYM
## Set up run_tests.sh and environmental variables
echo "export TESTBINPREFIX=$(top_srcdir)/src/c/breseq" > $(distdir)/tests/test.config;
echo "export BRESEQ_DATA_PATH=$(top_srcdir)/src/c/breseq" >> $(distdir)/tests/test.config;
echo "export BRESEQ_TEST_THREAD_ARG=\"-j 4\"" >> $(distdir)/tests/test.config;
echo "tests/test.sh clean tests" > ${distdir}/run_tests.sh
echo "tests/test.sh test tests" >> ${distdir}/run_tests.sh
chmod a+x ${distdir}/run_tests.sh
test:
## NEW method: 'make test' after 'make'
## This must be located here so that it is run after EXTRA_DIST files are included
echo "export TESTBINPREFIX=$(top_srcdir)/src/c/breseq" > $(top_srcdir)/tests/test.config;
echo "export BRESEQ_DATA_PATH=$(top_srcdir)/src/c/breseq" >> $(top_srcdir)/tests/test.config;
echo "export BRESEQ_TEST_THREAD_ARG=\"-j 4\"" >> $(top_srcdir)/tests/test.config;
$(top_srcdir)/tests/test.sh test tests
test-long:
## NEW method: 'make test' after 'make'
## This must be located here so that it is run after EXTRA_DIST files are included
echo "export TESTBINPREFIX=$(top_srcdir)/src/c/breseq" > $(top_srcdir)/tests/test.config;
echo "export BRESEQ_DATA_PATH=$(top_srcdir)/src/c/breseq" >> $(top_srcdir)/tests/test.config;
echo "export BRESEQ_TEST_THREAD_ARG=\"-j 4\"" >> $(top_srcdir)/tests/test.config;
$(top_srcdir)/tests/test.sh test tests long
clean-tests:
##This is commented out to not break make distcheck, which requires we not modify the source in this way?
##echo "export TESTBINPREFIX=$(top_srcdir)/src/c/breseq" > $(top_srcdir)/tests/test.config;
$(top_srcdir)/tests/test.sh clean tests long