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|
###################################################################
#
# The default compiler is GNU gcc/g++.
# Run
# make TRINITY_COMPILER=intel
# to build Inchworm and Chrysalis with the Intel compiler.
#
export TRINITY_HOME = $(PWD)
ifeq ($(TRINITY_COMPILER),intel)
INCHWORM_CONFIGURE_FLAGS = CXX=icpc CXXFLAGS="-fast"
CHRYSALIS_MAKE_FLAGS = COMPILER=icpc
else
override TRINITY_COMPILER=gnu
endif
all: inchworm_target chrysalis_target trinity_essentials
sh ./util/support_scripts/trinity_install_tests.sh
no_bamsifter: inchworm_target chrysalis_target
cd trinity-plugins && $(MAKE) no_bamsifter
install:
util/support_scripts/trinity_installer.py
inchworm_target:
@echo Using $(TRINITY_COMPILER) compiler for Inchworm and Chrysalis
cd Inchworm && $(MAKE)
chrysalis_target:
cd Chrysalis && $(MAKE)
trinity_essentials:
cd trinity-plugins && $(MAKE) trinity_essentials
plugins:
cd trinity-plugins && $(MAKE) plugins
sh ./util/support_scripts/plugin_install_tests.sh
test:
@echo
@echo "Checking for Trinity essentials (built from 'make all'):"
sh ./util/support_scripts/trinity_install_tests.sh
@echo
@echo "Checking for plugins (built from 'make plugins'):"
sh ./util/support_scripts/plugin_install_tests.sh
@echo "Run 'make test_trinity' if you want to test Trinity execution on a small data set"
clean:
cd Inchworm && $(MAKE) clean
cd Chrysalis && $(MAKE) clean
cd trinity-plugins && $(MAKE) clean
cd sample_data/ && $(MAKE) clean
test_trinity:
cd sample_data/test_Trinity_Assembly && $(MAKE) test
# note 'test_all': ** this is for a more advanced installation including devel features **
test_all:
cd sample_data/ && $(MAKE) test_all
./__pull_trinity_ext_sample_data.sh
cd trinity_ext_sample_data/ && $(MAKE) test
test_clean:
cd sample_data/ && $(MAKE) clean
cd trinity_ext_sample_data/ && $(MAKE) clean
###################################################################
|
