From 16eacdceadfda77e10208e65eb53cdb09ec2e1ae Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Sun, 27 Oct 2024 16:45:21 -0400
Subject: [PATCH] Modifications to facilitate installation

Modified the subdirectory for StxTyper to stx and modified the
github_binary target to enable the installation of combined
AMRFinderPlus and StxTyper.
---
 .gitmodules   |  2 +-
 Makefile      | 21 +++++++++++----------
 amrfinder.cpp |  2 +-
 stx           |  1 +
 stxtyper      |  1 -
 5 files changed, 14 insertions(+), 13 deletions(-)
 create mode 160000 stx
 delete mode 160000 stxtyper

diff --git a/.gitmodules b/.gitmodules
index 967e68e..34da84e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "stxtyper"]
-	path = stxtyper
+	path = stx
 	url = https://github.com/ncbi/stxtyper.git
diff --git a/Makefile b/Makefile
index 3e9fd13..112d885 100644
--- a/Makefile
+++ b/Makefile
@@ -153,12 +153,12 @@ mutate:	$(mutateOBJS)
 	$(CXX) -o $@ $(mutateOBJS)
 
 stxtyper:
-		$(MAKE) -C stxtyper
+		$(MAKE) -C stx
 
 clean:
 	rm -f *.o
 	rm -f $(BINARIES)
-	$(MAKE) -C stxtyper clean
+	$(MAKE) -C stx clean
 
 install:
 	@if [ ! -e $(DESTDIR)$(bindir) ]; \
@@ -166,7 +166,7 @@ install:
 		mkdir -p $(DESTDIR)$(bindir); \
 	fi
 	$(INSTALL) $(BINARIES) $(DESTDIR)$(bindir)
-	make -C stxtyper install PREFIX=$(PREFIX) bindir=$(bindir)
+	make -C stx install PREFIX=$(PREFIX) bindir=$(bindir)
 
 # amrfinder binaries for github binary release
 GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)
@@ -181,19 +181,20 @@ github_binaries:
 #   first recompile amrfinder.o to pick up the new version info
 #	and remove leaky NCBI paths
 	make clean
-	make all CXX=/usr/bin/g++ LD_RUN_PATH= -d
+	make all CXX=/usr/bin/g++ LD_RUN_PATH= 
 	mkdir $(GITHUB_FILE)
 	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
 	cp $(GITHUB_FILES) $(GITHUB_FILE)
-	make -C stxtyper install INSTALL_DIR=../$(GITHUB_FILE)/stxtyper
-	cp stxtyper/test_stxtyper.sh stxtyper/version.txt $(GITHUB_FILE)/stxtyper
-	mkdir $(GITHUB_FILE)/stxtyper/test
-	cp -R stxtyper/test/*.fa stxtyper/test/*.expected $(GITHUB_FILE)/stxtyper/test
+	make -C stx
+	make -C stx install INSTALL_DIR=../$(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 *
+	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
-	make -C stxtyper test
+	make -C stx test
 	./test_amrfinder.sh
diff --git a/amrfinder.cpp b/amrfinder.cpp
index bfbe5c3..fe158c4 100644
--- a/amrfinder.cpp
+++ b/amrfinder.cpp
@@ -845,7 +845,7 @@ struct ThisApplication : ShellApplication
     prog2dir ["amr_report"]    = execDir;	
 		prog2dir ["dna_mutation"]  = execDir;
     prog2dir ["fasta_extract"] = execDir;
-		prog2dir ["stxtyper"]      = execDir + "stxtyper/";
+		prog2dir ["stxtyper"]      = execDir + "stx/";
     
 
     if (pgap)
diff --git a/stx b/stx
new file mode 160000
index 0000000..3dede55
--- /dev/null
+++ b/stx
@@ -0,0 +1 @@
+Subproject commit 3dede555786e61abc04361d8b972c765031fe79c
diff --git a/stxtyper b/stxtyper
deleted file mode 160000
index ddc66ab..0000000
--- a/stxtyper
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ddc66abc95a0d74c4fbd0729dde1a7f772686b8d