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Makefile
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Makefile
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TOP_DIR = ../..
include $(TOP_DIR)/tools/Makefile.common
TARGET ?= /kb/deployment
DEPLOY_RUNTIME ?= /kb/runtime
SERVER_SPEC = GenomeAnnotation.spec
SERVICE_MODULE = lib/Bio/KBase/GenomeAnnotation/Service.pm
SERVICE = genome_annotation
SERVICE_PORT = 7050
# SERVICE_ALT_PORT = 7136
SERVICE_URL = https://kbase.us/services/$(SERVICE)
SERVICE_NAME = GenomeAnnotation
SERVICE_NAME_PY = $(SERVICE_NAME)
SERVICE_PSGI_FILE = $(SERVICE_NAME).psgi
SRC_SERVICE_PERL = $(wildcard service-scripts/*.pl)
BIN_SERVICE_PERL = $(addprefix $(BIN_DIR)/,$(basename $(notdir $(SRC_SERVICE_PERL))))
DEPLOY_SERVICE_PERL = $(addprefix $(SERVICE_DIR)/bin/,$(basename $(notdir $(SRC_SERVICE_PERL))))
ifdef TEMPDIR
TPAGE_TEMPDIR = --define kb_tempdir=$(TEMPDIR)
endif
ifdef SERVICE_ALT_PORT
TPAGE_SERVICE_ALT_PORT = --define kb_service_alt_port=$(SERVICE_ALT_PORT)
endif
KSER_PORT = 7106
KSER_DATA = /tmp/data
KSER_LOAD_THREADS = 8
KSER_KMER_THREADS = 12
KSER_FAMILY_THREADS = 4
KSER_INSERTER_THREADS = 4
ANNO_WORKERS = 6
ANNO_MAX_REQUESTS = 100
TPAGE_ARGS = --define kb_top=$(TARGET) \
--define kb_runtime=$(DEPLOY_RUNTIME) \
--define kb_service_name=$(SERVICE) \
--define kb_service_port=$(SERVICE_PORT) \
--define kb_starman_workers=$(ANNO_WORKERS) \
--define kb_starman_max_requests$(ANNO_MAX_REQUESTS) \
$(TPAGE_SERVICE_ALT_PORT) \
$(TPAGE_TEMPDIR) \
--define kser_port=$(KSER_PORT) \
--define kser_data=$(KSER_DATA) \
--define kser_load_threads=$(KSER_LOAD_THREADS) \
--define kser_kmer_threads=$(KSER_KMER_THREADS) \
--define kser_family_threads=$(KSER_FAMILY_THREADS) \
--define kser_inserter_threads=$(KSER_INSERTER_THREADS)
TESTS = $(wildcard t/client-tests/*.t)
all: bin compile-typespec service
test:
# run each test
echo "RUNTIME=$(DEPLOY_RUNTIME)\n"
for t in $(TESTS) ; do \
if [ -f $$t ] ; then \
$(DEPLOY_RUNTIME)/bin/perl $$t ; \
if [ $$? -ne 0 ] ; then \
exit 1 ; \
fi \
fi \
done
service: $(SERVICE_MODULE)
$(SERVICE_MODULE): $(SERVER_SPEC)
./recompile_typespec
compile-typespec: Makefile
mkdir -p lib/biokbase/$(SERVICE_NAME_PY)
touch lib/biokbase/__init__.py #do not include code in biokbase/__init__.py
touch lib/biokbase/$(SERVICE_NAME_PY)/__init__.py
mkdir -p lib/javascript/$(SERVICE_NAME)
compile_typespec \
--psgi $(SERVICE_PSGI_FILE) \
--impl Bio::KBase::$(SERVICE_NAME)::%sImpl \
--service Bio::KBase::$(SERVICE_NAME)::Service \
--client Bio::KBase::$(SERVICE_NAME)::Client \
--py biokbase/$(SERVICE_NAME_PY)/client \
--js javascript/$(SERVICE_NAME)/Client \
--url $(SERVICE_URL) \
--enable-retries \
$(SERVER_SPEC) lib
-rm -f lib/$(SERVER_MODULE)Server.py
-rm -f lib/$(SERVER_MODULE)Impl.py
-rm -f lib/CDMI_EntityAPIImpl.py
bin: $(BIN_PERL) $(BIN_DIR)/kmer_guts $(BIN_SERVICE_PERL)
$(BIN_DIR)/kmer_guts: src/kmer_guts
rm -f $(BIN_DIR)/kmer_guts
cp src/kmer_guts $(BIN_DIR)/kmer_guts
src/kmer_guts: src/kmer_guts.c
cd src; $(CC) $(CFLAGS) -O -o kmer_guts kmer_guts.c
deploy: deploy-client deploy-service
deploy-all: deploy-client deploy-service
deploy-client: compile-typespec deploy-docs deploy-libs deploy-scripts deploy-alt-scripts
RAST_SCRIPTS = $(filter scripts/rast2-%,$(SRC_PERL))
deploy-alt-scripts:
export KB_TOP=$(TARGET); \
export KB_RUNTIME=$(DEPLOY_RUNTIME); \
export KB_PERL_PATH=$(TARGET)/lib ; \
for src in $(RAST_SCRIPTS) ; do \
basefile=`basename $$src`; \
base=`basename $$src .pl`; \
alt=`echo $$base | sed 's/^rast2-/rast-/'`; \
echo install $$src $$alt ; \
cp $$src $(TARGET)/plbin ; \
$(WRAP_PERL_SCRIPT) "$(TARGET)/plbin/$$basefile" $(TARGET)/bin/$$alt ; \
done
deploy-guts: deploy-dir
rm -f $(TARGET)/services/$(SERVICE)/bin/kmer_guts
cp $(BIN_DIR)/kmer_guts $(TARGET)/services/$(SERVICE)/bin/kmer_guts
deploy-service: deploy-dir deploy-monit deploy-libs deploy-guts deploy-service-scripts
for templ in service/*.tt ; do \
base=`basename $$templ .tt` ; \
$(TPAGE) $(TPAGE_ARGS) $$templ > $(TARGET)/services/$(SERVICE)/$$base ; \
chmod +x $(TARGET)/services/$(SERVICE)/$$base ; \
done
deploy-service-scripts:
export KB_TOP=$(TARGET); \
export KB_RUNTIME=$(DEPLOY_RUNTIME); \
export KB_PERL_PATH=$(TARGET)/lib ; \
export PATH_PREFIX=$(TARGET)/services/$(SERVICE)/bin:$(TARGET)/services/cdmi_api/bin; \
for src in $(SRC_SERVICE_PERL) ; do \
basefile=`basename $$src`; \
base=`basename $$src .pl`; \
echo install $$src $$base ; \
cp $$src $(TARGET)/plbin ; \
$(WRAP_PERL_SCRIPT) "$(TARGET)/plbin/$$basefile" $(TARGET)/services/$(SERVICE)/bin/$$base ; \
done
deploy-monit:
$(TPAGE) $(TPAGE_ARGS) service/process.$(SERVICE).tt > $(TARGET)/services/$(SERVICE)/process.$(SERVICE)
deploy-docs:
-mkdir doc
-mkdir $(SERVICE_DIR)
-mkdir $(SERVICE_DIR)/webroot
mkdir -p doc
$(DEPLOY_RUNTIME)/bin/pod2html -t "Genome Annotation Service API" lib/Bio/KBase/GenomeAnnotation/GenomeAnnotationImpl.pm > doc/genomeanno_impl.html
cp doc/*html $(SERVICE_DIR)/webroot/.
deploy-dir:
if [ ! -d $(SERVICE_DIR) ] ; then mkdir $(SERVICE_DIR) ; fi
if [ ! -d $(SERVICE_DIR)/webroot ] ; then mkdir $(SERVICE_DIR)/webroot ; fi
if [ ! -d $(SERVICE_DIR)/bin ] ; then mkdir $(SERVICE_DIR)/bin ; fi
$(BIN_DIR)/%: service-scripts/%.pl $(TOP_DIR)/user-env.sh
$(WRAP_PERL_SCRIPT) '$$KB_TOP/modules/$(CURRENT_DIR)/$<' $@
$(BIN_DIR)/%: service-scripts/%.py $(TOP_DIR)/user-env.sh
$(WRAP_PYTHON_SCRIPT) '$$KB_TOP/modules/$(CURRENT_DIR)/$<' $@
include $(TOP_DIR)/tools/Makefile.common.rules