Upgrade to v0.5.2

.travis.yml

@@ -8,4 +8,4 @@ os:
 
 
 script:
-  - make linux
+  - make

Changelog

@@ -1,3 +1,7 @@
+v0.5.2
+    Support download via bioconda;
+    Use ghc::filesystem instead of std::filesystem for the cross-platform compatibility.
+
 v0.5.1
     Use robin_hood::unordered_map instead of std::unordered_map for performance improvement;
     The program rwr adds support for the weights and direction of the network;

INSTALL

@@ -1,10 +1,6 @@
 The GCEN requires compiler and library support for the ISO C++ 2017 standard.
 
-To compile the GCEN in Linux:
-make linux
+To compile the GCEN, please run the following command:
+make
 
-To compile the GCEN in macOS:
-make macos
-
-To compile the GCEN in Windows:
-make windows
+The executable files are located in the ./bin and ./util directory.

Makefile

@@ -1,63 +1,33 @@
-CXX = g++
-LFLAGS = -std=c++17 -static-libstdc++ -O3 -Wall
-MFLAGS = -std=c++17 -static-libgcc -O3 -Wall
-WFLAGS = -std=c++17 -static -O3 -Wall
-
-
-linux: 
-	mkdir -p bin
-	mkdir -p util
-
-	$(CXX) src/data_norm.cpp -o bin/data_norm $(LFLAGS)
-	$(CXX) src/data_filter.cpp -o bin/data_filter $(LFLAGS)
-	$(CXX) src/network_build.cpp -o bin/network_build -pthread $(LFLAGS)
-	$(CXX) src/module_identify.cpp -o bin/module_identify -pthread $(LFLAGS)
-	$(CXX) src/annotate.cpp -o bin/annotate -pthread -lstdc++fs $(LFLAGS)
-	$(CXX) src/rwr.cpp -o bin/rwr $(LFLAGS)
-
-	$(CXX) src/data_stat.cpp -o util/data_stat $(LFLAGS)
-	$(CXX) src/network_merge.cpp -o util/network_merge $(LFLAGS)
-	$(CXX) src/enrich.cpp -o util/enrich $(LFLAGS)
-	$(CXX) src/generate_expr_matrix_from_rsem.cpp -o util/generate_expr_matrix_from_rsem $(LFLAGS)
-	$(CXX) src/generate_expr_matrix_from_stringtie.cpp -o util/generate_expr_matrix_from_stringtie $(LFLAGS)
-
-
-macos: 
-	mkdir -p bin
-	mkdir -p util
-
-	$(CXX) src/data_norm.cpp -o bin/data_norm $(MFLAGS)
-	$(CXX) src/data_filter.cpp -o bin/data_filter $(MFLAGS)
-	$(CXX) src/network_build.cpp -o bin/network_build -pthread $(MFLAGS)
-	$(CXX) src/module_identify.cpp -o bin/module_identify -pthread $(MFLAGS)
-	$(CXX) src/annotate.cpp -o bin/annotate -pthread -lstdc++fs $(MFLAGS)
-	$(CXX) src/rwr.cpp -o bin/rwr $(MFLAGS)
-
-	$(CXX) src/data_stat.cpp -o util/data_stat $(MFLAGS)
-	$(CXX) src/network_merge.cpp -o util/network_merge $(MFLAGS)
-	$(CXX) src/enrich.cpp -o util/enrich $(MFLAGS)
-	$(CXX) src/generate_expr_matrix_from_rsem.cpp -o util/generate_expr_matrix_from_rsem $(MFLAGS)
-	$(CXX) src/generate_expr_matrix_from_stringtie.cpp -o util/generate_expr_matrix_from_stringtie $(MFLAGS)
-
-
-windows: 
-	mkdir -p bin
-	mkdir -p util
-
-	$(CXX) src/data_norm.cpp -o bin/data_norm $(WFLAGS)
-	$(CXX) src/data_filter.cpp -o bin/data_filter $(WFLAGS)
-	$(CXX) src/network_build.cpp -o bin/network_build -pthread $(WFLAGS)
-	$(CXX) src/module_identify.cpp -o bin/module_identify -pthread $(WFLAGS)
-	$(CXX) src/annotate.cpp -o bin/annotate -pthread -lstdc++fs $(WFLAGS)
-	$(CXX) src/rwr.cpp -o bin/rwr $(WFLAGS)
-
-	$(CXX) src/data_stat.cpp -o util/data_stat $(WFLAGS)
-	$(CXX) src/network_merge.cpp -o util/network_merge $(WFLAGS)
-	$(CXX) src/enrich.cpp -o util/enrich $(WFLAGS)
-	$(CXX) src/generate_expr_matrix_from_rsem.cpp -o util/generate_expr_matrix_from_rsem $(WFLAGS)
-	$(CXX) src/generate_expr_matrix_from_stringtie.cpp -o util/generate_expr_matrix_from_stringtie $(WFLAGS)
-
-
-clean:
-	rm -rf bin
-	rm -rf util
+PREFIX = .
+CCFLAGS = -std=c++17 -O3 -Wall
+
+
+ifeq ($(OS),Windows_NT)
+	CCFLAGS += -static -D AMD64
+else
+	UNAME_S := $(shell uname -s)
+	ifeq ($(UNAME_S),Linux)
+		CCFLAGS += -static-libstdc++ -D LINUX
+	endif
+	ifeq ($(UNAME_S),Darwin)
+		CCFLAGS += -D OSX
+	endif
+endif
+
+
+all:
+	mkdir -p $(PREFIX)/bin
+	mkdir -p $(PREFIX)/util
+
+	$(CXX) src/data_norm.cpp -o $(PREFIX)/bin/data_norm $(CCFLAGS)
+	$(CXX) src/data_filter.cpp -o $(PREFIX)/bin/data_filter $(CCFLAGS)
+	$(CXX) src/network_build.cpp -o $(PREFIX)/bin/network_build -pthread $(CCFLAGS)
+	$(CXX) src/module_identify.cpp -o $(PREFIX)/bin/module_identify -pthread $(CCFLAGS)
+	$(CXX) src/annotate.cpp -o $(PREFIX)/bin/annotate -pthread $(CCFLAGS)
+	$(CXX) src/rwr.cpp -o $(PREFIX)/bin/rwr $(CCFLAGS)
+
+	$(CXX) src/data_stat.cpp -o $(PREFIX)/util/data_stat $(CCFLAGS)
+	$(CXX) src/network_merge.cpp -o $(PREFIX)/util/network_merge $(CCFLAGS)
+	$(CXX) src/enrich.cpp -o $(PREFIX)/util/enrich $(CCFLAGS)
+	$(CXX) src/generate_expr_matrix_from_rsem.cpp -o $(PREFIX)/util/generate_expr_matrix_from_rsem $(CCFLAGS)
+	$(CXX) src/generate_expr_matrix_from_stringtie.cpp -o $(PREFIX)/util/generate_expr_matrix_from_stringtie $(CCFLAGS)

README.md

@@ -1,4 +1,4 @@
-## GCEN: an easy toolkit of Gene Co-Expression Network analysis for lncRNA annotation  
+## GCEN: an easy toolkit of Gene Co-Expression Network analysis for lncRNAs annotation  
 
 [![platforms](https://img.shields.io/badge/platforms-Linux%20%7C%20macOS%20%7C%20Windows-yellowgreen)](https://www.biochen.org/gcen/)
 [![release version](https://img.shields.io/github/v/release/wen-chen/gcen)](https://www.biochen.org/gcen)
@@ -243,4 +243,4 @@ rwr -n ../sample_data/gene_co_expr.network -g ../sample_data/rwr_interested_gene
 To understand the format of the input and output files for each program, please take a look at the sample data included in the software package.  
 
 #### Contact  
-Wen Chen,     Ph.D. Candidate,     [email protected]
+Wen Chen,     Ph.D. Candidate,     [email protected]

src/annotate.cpp

@@ -4,15 +4,15 @@
 #include <iostream>
 #include <vector>
 #include <unordered_map>
-#include <experimental/filesystem> // -std=c++17 -lstdc++fs
 #include <thread> // Multithreading
+#include "third_party/ghc/filesystem.hpp"
 #include "util/func.hpp"
 #include "util/enrich_util.hpp"
 #include "util/hypergeometric_p_value.hpp"
 
 
 void go_annot_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "annotate usage:\n";
   std::cout << "  annotate -g go-basic.obo -a gene_go_association_file -n input_network -o out_dir\n";
   std::cout << "options:\n";
@@ -71,7 +71,7 @@ void module_kegg_annotate(int n, int thread_num, std::vector <std::unordered_set
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     go_annot_help();
-    return -1;
+    return 0;
   }
 
   // get options
@@ -175,7 +175,7 @@ int main(int argc, char* argv[]) {
     propagate(assoc_map, go_term_map);
 
     // mkdir
-    std::experimental::filesystem::create_directories(out_dir);
+    ghc::filesystem::create_directories(out_dir);
 
     // annotation
     std::unordered_set <std::string> background_gene_set;
@@ -235,7 +235,7 @@ int main(int argc, char* argv[]) {
     assoc_parser(assoc_file_name, K_map, assoc_map);
 
     // mkdir
-    std::experimental::filesystem::create_directories(out_dir);
+    ghc::filesystem::create_directories(out_dir);
 
     // annotate
     std::unordered_set <std::string> background_gene_set;

src/data_filter.cpp

@@ -6,7 +6,7 @@
 
 
 void data_filter_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "data_filter usage:\n";
   std::cout << "  data_filter -i input_file -o output_file\n";
   std::cout << "options:\n";
@@ -26,7 +26,7 @@ void data_filter_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     data_filter_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/data_norm.cpp

@@ -5,7 +5,7 @@
 
 
 void data_norm_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "data_norm usage:\n";
   std::cout << "  data_norm -i input_file -o output_file -m normalization_method\n";
   std::cout << "options:\n";
@@ -22,7 +22,7 @@ void data_norm_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     data_norm_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/data_stat.cpp

@@ -6,7 +6,7 @@
 
 
 void data_stat_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "data_stat usage:\n";
   std::cout << "  data_stat -i input_file\n";
   std::cout << "options:\n";
@@ -21,7 +21,7 @@ void data_stat_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     data_stat_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/enrich.cpp

@@ -11,7 +11,7 @@
 
 
 void enrich_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "enrich usage:\n";
   std::cout << "  enrich -e enrichment_gene_list_file -b background_gene_list_file -g go-basic.obo "
                "-a gene_go_association_file -p p_value_cutoff -o out_put_file\n";
@@ -36,7 +36,7 @@ void enrich_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     enrich_help();
-    return -1;
+    return 0;
   }
 
   // get options

src/generate_expr_matrix_from_rsem.cpp

@@ -9,7 +9,7 @@
 
 
 void rsem_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "generate_expr_matrix_from_rsem usage:\n";
   std::cout << "  generate_expr_matrix_from_rsem -i input_file -o output_file\n";
   std::cout << "options:\n";
@@ -30,7 +30,7 @@ void read_sample_file(std::string sample_file_name, int i, std::string flag,
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     rsem_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/generate_expr_matrix_from_stringtie.cpp

@@ -10,7 +10,7 @@
 
 
 void stringtie_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "generate_expr_matrix_from_stringtie usage:\n";
   std::cout << "  generate_expr_matrix_from_stringtie -i input_file -o output_file\n";
   std::cout << "options:\n";
@@ -32,7 +32,7 @@ void read_sample_file(std::string sample_file_name, int i, std::string flag,
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     stringtie_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/module_identify.cpp

@@ -16,7 +16,7 @@ static std::mutex mutex_lock;
 
 
 void module_identify_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "module_identify usage:\n";
   std::cout << "  module_identify -i input_file -o output_file\n";
   std::cout << "options:\n";
@@ -128,7 +128,7 @@ void ThreadFunc(int n, int thread_num, std::vector <std::string> & node_vec,
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     module_identify_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/network_build.cpp

@@ -12,7 +12,7 @@
 
 
 void network_build_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "network_build usage:\n";
   std::cout << "  network_build -i gene_expression_file -o co_expression_network_file\n";
   std::cout << "options:\n";
@@ -45,7 +45,7 @@ void ThreadFunc_FDR(int n, int thread_num, int GeneNum, int SampleNum, std::vect
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     network_build_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/network_merge.cpp

@@ -6,7 +6,7 @@
 
 
 void network_merge_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "network_merge usage:\n";
   std::cout << "  network_merge -i input_files -o output_file\n";
   std::cout << "options:\n";
@@ -22,7 +22,7 @@ void network_merge_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     network_merge_help();
-    return -1;
+    return 0;
   }
 
   // get option

src/rwr.cpp

@@ -5,7 +5,7 @@
 
 
 void rwr_help() {
-  std::cout << "GCEN 0.5.1 by Wen Chen ([email protected], https://www.biochen.com/gcen)\n";
+  std::cout << version;
   std::cout << "rwr usage:\n";
   std::cout << "  rwr -n input_network -g gene_list -o output_result\n";
   std::cout << "options:\n";
@@ -27,7 +27,7 @@ void rwr_help() {
 int main(int argc, char* argv[]) {
   if (argc < 2) {
     rwr_help();
-    return -1;
+    return 0;
   }
 
   // get option