Merge remote-tracking branch 'refs/remotes/origin/main' into pages

Author: endixk

.gitignore

@@ -5,14 +5,14 @@
 
 EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis and dendrogram representation.
 
- * [Homepage](http://leb.snu.ac.kr/ezaai)
+ * [Homepage](http://endixk.github.io/ezaai)
  * [Publication](https://doi.org/10.1007/s12275-021-1154-0)
 
 
 ## Quick start with conda
 
 ~~~bash
-conda install -c bioconda -y ezaai
+conda install -c bioconda ezaai
 ezaai -h
 ~~~
 
@@ -29,16 +29,16 @@ java -jar target/EzAAI-*.jar -h
 
 ## Available modules
 ### `extract`
- * Extract protein database from genome using Prodigal
+ * Extract protein database(s) from genome using Prodigal
 
 ~~~bash
 ezaai extract -i <IN_SEQ> -o <OUT_DB>
 ~~~
 
 |Argument|Description|
 |:-:|-----------------|
-|`-i`|Input prokaryotic genome sequence|
-|`-o`|Output database|
+|`-i`|Input file or directory with prokaryotic genome sequence(s)|
+|`-o`|Output file or directory|
 
 ---
 

README.md

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>EzAAI</groupId>
     <artifactId>EzAAI</artifactId>
-    <version>1.2.3</version>
+    <version>1.2.4</version>
 
     <dependencies>
         <dependency>

pom.xml

@@ -31,13 +31,13 @@
 import java.util.concurrent.Future;
 
 public class EzAAI {
-	public static final String VERSION  = "v1.2.3",
-							   RELEASE  = "Feb. 2024",
+	public static final String VERSION  = "v1.2.4",
+							   RELEASE  = "Jul. 2025",
 							   CITATION = " Kim, D., Park, S. & Chun, J.\n"
 							   			+ " Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity.\n"
 							   			+ " J Microbiol. 59, 476–480 (2021).\n"
 							   			+ " DOI: 10.1007/s12275-021-1154-0";
-	public static final boolean STABLE  = false;
+	public static final boolean STABLE  = true;
 
 	final static int MODULE_CONVERT 	= 1,
 					 MODULE_EXTRACT 	= 2,
@@ -143,6 +143,14 @@ private int parseArguments(String[] args) {
 			} else {
 				String path = new File(output).getAbsolutePath();
 				String parent = path.substring(0, path.lastIndexOf(File.separator));
+				if(!(new File(parent)).exists()) {
+					if(!(new File(parent)).mkdirs()) {
+						Prompt.error("Failed to create parent directory for the output file: " + parent);
+						return -1;
+					} else {
+						Prompt.talk("Created parent directory for the output file: " + parent);
+					}
+				}
 				if(!(new File(parent)).canWrite()) {
 					Prompt.error("Output file is allocated to a non-writable directory: " + parent);
 					return -1;