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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
PACKAGEDIR = $(top_srcdir)/package
MACPACKAGEDIR = $(PACKAGEDIR)/macosx
MACPACKAGEBUILDDIR = $(MACPACKAGEDIR)/build
SUBDIRS = $(LIBBAM) $(BRESEQ)
### Tests! -- only one test included for now in distribution.
EXTRA_DIST = \
tests/common.sh \
tests/test.sh \
tests/lambda_mult_ref_read/expected.gd \
tests/lambda_mult_ref_read/testcmd.sh \
tests/data/lambda/lambda_mixed_population.1.fastq \
tests/data/lambda/lambda_mixed_population.2.fastq \
tests/data/lambda/lambda_mixed_population.3.fastq \
tests/data/lambda/lambda_mixed_population.4.fastq \
tests/data/lambda/lambda_mixed_population.5.fastq \
tests/data/lambda/lambda.1-2.gbk \
tests/data/lambda/lambda.3.gbk \
tests/data/lambda/lambda.4.gbk \
tests/data/lambda/lambda.5.gbk \
src/doc/Makefile \
src/doc/conf.py \
src/doc/acknowledgments.rst \
src/doc/faq.rst \
src/doc/gd_format.rst \
src/doc/gd_usage.rst \
src/doc/index.rst \
src/doc/installation.rst \
src/doc/introduction.rst \
src/doc/methods.rst \
src/doc/output.rst \
src/doc/references.rst \
src/doc/test_drive.rst \
src/doc/usage.rst \
src/doc/images \
src/doc/images/amp_1.png \
src/doc/images/breseq.png \
src/doc/images/coverage_distribution.png \
src/doc/images/del_1.png \
src/doc/images/del_2.png \
src/doc/images/end_trimming_example.docx \
src/doc/images/end_trimming_example.png \
src/doc/images/error_rates.png \
src/doc/images/ins_1.png \
src/doc/images/ins_2.png \
src/doc/images/jc_1.png \
src/doc/images/jc_2.png \
src/doc/images/mc_1.png \
src/doc/images/missed_mutation_no_trimming.png \
src/doc/images/mob_1.png \
src/doc/images/mob_2.png \
src/doc/images/mob_3.png \
src/doc/images/ra_1.png \
src/doc/images/region_coverage_example.png \
src/doc/images/snp_1.png \
src/doc/images/snp_2.png \
src/doc/images/sub_1.png
## tests - does not work yet.
##TESTS_ENVIRONMENT = PROGRAMDATAPATH=$(BRESEQ) SAMTOOLSPATH=$(SAMTOOLSDIR)
##TESTS = tests/lambda_mult_ref_read/testcmd.sh
DOCSRCDIR=$(top_srcdir)/src/doc
DOCBUILDDIR=$(abs_top_builddir)/src/doc/_build
PERLGENOMEDIFF=$(top_srcdir)/src/perl/GenomeDiff
SAMTOOLSDIR=$(top_srcdir)/$(LIBBAM)
## Main hooks called after normal make steps
all-local :
## We should build Perl modules here (and not during install) because
## otherwise a sudo make install creates superuser owned files in the
## distribution, that are not removed by make clean.
## OLD method: 'make test' after 'make install'
## This saves the install path for the test script
##echo "export TESTBINPREFIX=$(bindir)" > tests/test.config;
install-exec-local :
clean-local :: clean-tests
## This saves the install path for the test script
rm -f tests/test.config
## These two targets are optional for Perl genomediff tools.
genomediff :
## GenomeDiff
cd $(PERLGENOMEDIFF) ; \
perl Build.PL --install_base=$(prefix) --install_path bin=$(bindir) --install_path script=$(bindir) ; \
./Build install;
clean-genomediff :
## GenomeDiff
cd $(PERLGENOMEDIFF) ; \
./Build clean;
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: docs
## This environmental variable is used by python Sphinx
cp -r $(DOCBUILDDIR)/html $(distdir)/documentation ;
## GenomeDiff
cd $(abs_top_srcdir)/src/perl/GenomeDiff ; \
chmod u+w . ; \
perl Build.PL ; \
./Build distdir ;
mkdir -p $(distdir)/src/perl
cp -r $(abs_top_srcdir)/src/perl/GenomeDiff/GenomeDiff-* $(distdir)/src/perl/GenomeDiff ;
## Remove ._ files
rm -rf `find $(distdir) -name ".*"`
macosx-pkg-download :
mkdir -p $(PACKAGEDIR)
mkdir -p $(MACPACKAGEDIR)
cd $(MACPACKAGEDIR) ; \
curl -O ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_mac.tgz ; \
tar -xvzf ssaha2_mac.tgz;
macosx-pkg-compile :
mkdir -p $(MACPACKAGEBUILDDIR)
cp $(MACPACKAGEDIR)/ssaha2*/ssaha2* $(MACPACKAGEBUILDDIR)/bin ;
## Install outselves into this dir
./configure --prefix=$(MACPACKAGEBUILDDIR) ; \
make install ;
clean-pkg :
rm -rf package
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" >> $(top_srcdir)/tests/test.config;
echo "export BRESEQ_SAMTOOLS_PATH=$(top_srcdir)/extern/samtools-0.1.18" >> $(top_srcdir)/tests/test.config;
$(top_srcdir)/tests/test.sh test tests
clean-tests:
$(top_srcdir)/tests/test.sh clean tests
distclean-local:
rm -rf $(DOCBUILDDIR);