Changes version to 1.6.0

README.md

@@ -33,4 +33,3 @@ Please, cite the following publication if you use SEDA:
 ## Credits
 
 The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
-

pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.sing_group</groupId>
 	<artifactId>seda-all</artifactId>
-	<version>1.6.0-SNAPSHOT</version>
+	<version>1.6.0</version>
 	<packaging>pom</packaging>
 
 	<name>SEquence DAtaset builder</name>
@@ -41,18 +41,22 @@
 			<name>Miguel Reboiro-Jato</name>
 			<organization>SING Group - University of Vigo</organization>
 			<organizationUrl>http://www.sing-group.org</organizationUrl>
-			<email>mrjato@uvigo.es</email>
+			<email>mrjato@uvigo.gal</email>
 		</developer>
 		<developer>
 			<name>Hugo López-Fernández</name>
 			<organization>SING Group - University of Vigo</organization>
 			<organizationUrl>http://www.sing-group.org</organizationUrl>
-			<email>hlfernandez@uvigo.es</email>
+			<email>hlfernandez@uvigo.gal</email>
 		</developer>
 		<developer>
 			<name>David Vila Fernández</name>
 			<organization>Escola Superior de Enxeñaría Informática - University of Vigo</organization>
 		</developer>
+		<developer>
+			<name>Miguel José da Silva Araújo</name>
+			<organization>Escola Superior de Enxeñaría Informática - University of Vigo</organization>
+		</developer>
 	</developers>
 
 	<contributors>
@@ -86,7 +90,7 @@
 
 		<!-- Dependencies -->
 		<yacli.version>2.3.0-SNAPSHOT</yacli.version>
-		<gc4s.version>1.7.0-SNAPSHOT</gc4s.version>
+		<gc4s.version>1.7.0</gc4s.version>
 		<jsoup.version>1.8.3</jsoup.version>
 		<commons-csv.version>1.2.0</commons-csv.version>
 		<moxy.version>2.5.2</moxy.version>

seda-distribution/resources/seda-cli-distributable-choices.xml

@@ -10,12 +10,12 @@
   it under the terms of the GNU General Public License as
   published by the Free Software Foundation, either version 3 of the
   License, or (at your option) any later version.
-  
+
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
-  
+
   You should have received a copy of the GNU General Public
   License along with this program.  If not, see
   <http://www.gnu.org/licenses/gpl-3.0.html>.

seda-distribution/resources/seda-gui-distributable-choices.xml

@@ -10,12 +10,12 @@
   it under the terms of the GNU General Public License as
   published by the Free Software Foundation, either version 3 of the
   License, or (at your option) any later version.
-  
+
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
-  
+
   You should have received a copy of the GNU General Public
   License along with this program.  If not, see
   <http://www.gnu.org/licenses/gpl-3.0.html>.

seda-docker/Dockerfile.local

@@ -15,7 +15,7 @@ RUN apt-get update && apt-get install -y \
 		stable" && \
 	apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io
 
-COPY seda-linux-64b-1.6.0-SNAPSHOT.tar.gz /tmp/SEDA.tar.gz
+COPY seda-linux-64b-1.6.0.tar.gz /tmp/SEDA.tar.gz
 
 RUN mkdir /opt/SEDA && tar zxvf /tmp/SEDA.tar.gz -C /opt/SEDA && rm /tmp/SEDA.tar.gz
 

seda-docker/README.md

@@ -15,13 +15,13 @@ To increase the RAM memory that the dockerized version of SEDA for Linux systems
 
 # Running the SEDA CLI in Linux
 
-SEDA 1.6.0 introduces a new Command-Line Interface (CLI). This CLI is currently under development and most operations have been already implemented. 
+SEDA 1.6.0 introduced a new Command-Line Interface (CLI).
 
-To see the `SEDA` help and obtain the list of available commands, just run `docker run --rm pegi3s/seda:1.6.0-v2304 /opt/SEDA/run-cli.sh help`. 
+To see the `SEDA` help and obtain the list of available commands, just run `docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help`.
 
-And to obtain the help of a specific command, just run  `docker run --rm pegi3s/seda:1.6.0-v2304 /opt/SEDA/run-cli.sh help <command>` (e.g.  `docker run --rm pegi3s/seda:1.6.0-v2304  /opt/SEDA/run-cli.sh help sort`)
+And to obtain the help of a specific command, just run  `docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help <command>` (e.g. `docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help sort`)
 
-You should adapt and run the following command: `docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0-v2304 /opt/SEDA/run-cli.sh <command> -if /data/input.fasta -od /data/output <command_parameters>`
+You should adapt and run the following command: `docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh <command> -if /data/input.fasta -od /data/output <command_parameters>`
 
 In this command, you should replace:
 - `/your/data/dir` to point to the directory that contains the input file you want to process with SEDA.
@@ -30,4 +30,4 @@ In this command, you should replace:
 - `<command>` to the SEDA command you want to execute.
 - `<command_parameters>` to the list of command parameters.
 
-For instance, in order to sort a FASTA file, you should run: `docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0-v2304 /opt/SEDA/run-cli.sh sort -if /data/input.fasta -od /data/output --sort-on header --descending --criteria alphabetical`
+For instance, in order to sort a FASTA file, you should run: `docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh sort -if /data/input.fasta -od /data/output --sort-on header --descending --criteria alphabetical`

seda-docker/docker-compose.yml

@@ -1,7 +1,7 @@
 version: "3.3"
 services:
   seda:
-    image: pegi3s/seda:1.6.0-SNAPSHOT
+    image: pegi3s/seda:1.6.0
     build:
       context: ./
       dockerfile: Dockerfile.local

seda-plugin-bedtools/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-blast/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-cga/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-clustalomega/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-emboss/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-pfam/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-prosplign-procompart/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-        <version>1.6.0-SNAPSHOT</version>
+        <version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-sapp/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-splign-compart/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.6.0-SNAPSHOT</version>
+		<version>1.6.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>