Merge pull request #154 from ncbi/stxtype

Release 4.0.3

Author: evolarjun

.github/workflows/ccpp.yml

@@ -17,6 +17,8 @@ jobs:
       run: |
           sudo apt-get update
           sudo apt-get install -y hmmer ncbi-blast+ git libcurl4-openssl-dev build-essential curl
+    - name: submodule checkout
+      run: git submodule update --init --recursive
     - name: make
       run: cat version.txt; make
     - name: download db
@@ -26,12 +28,10 @@ jobs:
     - name: make test
       run: make test
     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
-      run: |
-          ./amrfinder -u 2>&1 | tee output
-          fgrep 'Skipping update, use amrfinder --force_update to overwrite the existing database' output
+      run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
     - name: make github_binaries
       run: make github_binaries
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
           name: release-binary
           path: amrfinder_binaries_v*.tar.gz

.github/workflows/mac_ccpp.yml

@@ -13,6 +13,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+    - name: submodule checkout
+      run: git submodule update --init --recursive
     - name: prerequisites
       run: |
           /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
@@ -29,13 +31,13 @@ jobs:
     - name: make test
       run: make test
     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
-      run: ./amrfinder -u 2>&1 | fgrep 'Skipping update, use amrfinder --force_update to overwrite the existing database'
+      run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
     - name: make github_binaries
       run: |
           make github_binaries
           version=`cat version.txt`
           mv amrfinder_binaries_v$version.tar.gz amrfinder_binaries_osx_v$version.txt
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
           name: release-binary
           path: amrfinder_binaries_osx_v*.tar.gz

.gitignore

@@ -2,12 +2,13 @@ data/
 *.o
 amr_report
 amrfinder
-fasta_check
-fasta_extract
-dna_mutation
-gff_check
 amrfinder_index
 amrfinder_update
 amrfinder_customize
+dna_mutation
+fasta_check
+fasta_extract
 fasta2parts
+gff_check
+mutate
 *.got

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "stxtyper"]
+	path = stx
+	url = https://github.com/ncbi/stxtyper.git

Makefile

@@ -81,11 +81,12 @@ CXX=g++
 COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c 
 
 
-.PHONY: all clean install release 
+.PHONY: all clean install release stxtyper test
 
-BINARIES= amr_report amrfinder amrfinder_index amrfinder_update fasta_check fasta_extract fasta2parts gff_check dna_mutation 
+BINARIES= amr_report amrfinder amrfinder_index amrfinder_update fasta_check \
+		  fasta_extract fasta2parts gff_check dna_mutation mutate
 
-all:	$(BINARIES)
+all:	$(BINARIES) stxtyper
 
 release: clean
 	svnversion . > version.txt
@@ -95,18 +96,19 @@ common.o:	common.hpp common.inc
 curl_easy.o: curl_easy.hpp common.hpp common.inc
 gff.o: gff.hpp common.hpp common.inc
 alignment.o:	alignment.hpp alignment.hpp common.inc
+seq.o: seq.hpp common.hpp common.inc
 
-amr_report.o:	common.hpp common.inc gff.hpp alignment.hpp
+amr_report.o:	common.hpp common.inc gff.hpp alignment.hpp tsv.hpp columns.hpp version.txt
 amr_reportOBJS=amr_report.o common.o gff.o alignment.o
 amr_report:	$(amr_reportOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(amr_reportOBJS)
 
-amrfinder.o:  common.hpp common.inc gff.hpp
+amrfinder.o:  common.hpp common.inc gff.hpp tsv.hpp columns.hpp version.txt
 amrfinderOBJS=amrfinder.o common.o gff.o tsv.o
 amrfinder:	$(amrfinderOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(amrfinderOBJS) -pthread $(DBDIR)
 
-amrfinder_update.o:  common.hpp common.inc 
+amrfinder_update.o:  common.hpp common.inc curl_easy.hpp version.txt
 amrfinder_updateOBJS=amrfinder_update.o common.o curl_easy.o
 amrfinder_update:      $(amrfinder_updateOBJS) 
 	@if [ "$(TEST_UPDATE)" != "" ]  ; \
@@ -115,69 +117,84 @@ amrfinder_update:      $(amrfinder_updateOBJS)
 	fi # make sure the next make command rebuilds amrfinder_update
 	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_updateOBJS) -lcurl 
 
-amrfinder_index.o:  common.hpp common.inc 
+amrfinder_index.o:  common.hpp common.inc version.txt
 amrfinder_indexOBJS=amrfinder_index.o common.o
 amrfinder_index:      $(amrfinder_indexOBJS) 
 	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_indexOBJS) 
 
-fasta_check.o:	common.hpp common.inc 
+fasta_check.o:	common.hpp common.inc version.txt
 fasta_checkOBJS=fasta_check.o common.o 
 fasta_check:	$(fasta_checkOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(fasta_checkOBJS)
 
-fasta_extract.o:	common.hpp common.inc
+fasta_extract.o:	common.hpp common.inc version.txt
 fasta_extractOBJS=fasta_extract.o common.o
 fasta_extract:	$(fasta_extractOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(fasta_extractOBJS)
 
-fasta2parts.o:	common.hpp common.inc
+fasta2parts.o:	common.hpp common.inc version.txt
 fasta2partsOBJS=fasta2parts.o common.o
 fasta2parts:	$(fasta2partsOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(fasta2partsOBJS)
 
-gff_check.o:	common.hpp common.inc gff.hpp
+gff_check.o:	common.hpp common.inc gff.hpp version.txt
 gff_checkOBJS=gff_check.o common.o gff.o
 gff_check:	$(gff_checkOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(gff_checkOBJS)
 
-dna_mutation.o:	common.hpp common.inc alignment.hpp
+dna_mutation.o:	common.hpp common.inc alignment.hpp tsv.hpp columns.hpp version.txt
 dna_mutationOBJS=dna_mutation.o common.o alignment.o
 dna_mutation:	$(dna_mutationOBJS)
 	$(CXX) $(LDFLAGS) -o $@ $(dna_mutationOBJS)
 
+mutate.o:	common.hpp common.inc alignment.hpp seq.hpp version.txt
+mutateOBJS=mutate.o common.o alignment.o seq.o
+mutate:	$(mutateOBJS)
+	$(CXX) -o $@ $(mutateOBJS)
 
+stxtyper:
+		$(MAKE) -C stx
 
 clean:
 	rm -f *.o
 	rm -f $(BINARIES)
+	$(MAKE) -C stx clean
 
 install:
 	@if [ ! -e $(DESTDIR)$(bindir) ]; \
 	then \
 		mkdir -p $(DESTDIR)$(bindir); \
 	fi
 	$(INSTALL) $(BINARIES) $(DESTDIR)$(bindir)
+	make -C stx install PREFIX=$(PREFIX) bindir=$(bindir)
 
 # amrfinder binaries for github binary release
 GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)
 GITHUB_FILES = test_amrfinder.sh test_*.expected test_*.fa test_*.gff $(BINARIES)
+
 github_binaries:
 	@if [ ! -e version.txt ]; \
 	then \
 		echo >&2 "version.txt required to make a distribution file"; \
 		false; \
 	fi
 #   first recompile amrfinder.o to pick up the new version info
-	rm amrfinder.o amrfinder
-	make
+#	and remove leaky NCBI paths
+	make clean
+	make all CXX=/usr/bin/g++ LD_RUN_PATH= 
 	mkdir $(GITHUB_FILE)
 	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
 	cp $(GITHUB_FILES) $(GITHUB_FILE)
+	make -C stx
+	make -C stx install INSTALL_DIR=../$(GITHUB_FILE)/stx CXX=/usr/bin/g++ LD_RUN_PATH=
+	cp stx/test_stxtyper.sh stx/version.txt $(GITHUB_FILE)/stx
+	mkdir $(GITHUB_FILE)/stx/test
+	cp -R stx/test/*.fa stx/test/*.expected $(GITHUB_FILE)/stx/test
 	if [ -e $(GITHUB_FILE).tar.gz ]; then rm $(GITHUB_FILE).tar.gz; fi
-	cd $(GITHUB_FILE); tar cvfz ../$(GITHUB_FILE).tar.gz *
-#	tar cvfz $(GITHUB_FILE).tar.gz $(GITHUB_FILE)/*
+	cd $(GITHUB_FILE); ln -s stx/stxtyper .; tar cvfz ../$(GITHUB_FILE).tar.gz *
 	rm -r $(GITHUB_FILE)/*
 	rmdir $(GITHUB_FILE)
 
-test : $(DISTFILES) Makefile *.cpp *.hpp *.inc test_dna.fa test_prot.fa test_prot.gff test_dna.fa test_dna.expected test_prot.expected test_both.expected
+test: $(DISTFILES) Makefile *.cpp *.hpp *.inc test_dna.fa test_prot.fa test_prot.gff test_dna.fa test_dna.expected test_prot.expected test_both.expected
+	make -C stx test
 	./test_amrfinder.sh

README.md

@@ -1,3 +1,17 @@
+# WARNING: This is an experimental version that includes StxTyper
+
+Currently it will need to be compiled from source to install.
+
+### Downloading and compiling AMRFinderPlus with StxTyper
+
+    git clone https://github.com/ncbi/amr.git
+    cd amr
+    git checkout stxtype
+    git submodule update --init
+    make
+    ./amrfinder -u
+    make test
+
 # NCBI Antimicrobial Resistance Gene Finder (AMRFinderPlus)
 
 This software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. We have also added "plus" stress, heat, and biocide resistance and virulence factors for [some organisms](https://github.com/evolarjun/amr/wiki/Curated-organisms).