diff --git a/README.md b/README.md index 39b9234..24fd05d 100644 --- a/README.md +++ b/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. - diff --git a/pom.xml b/pom.xml index bc17adb..3cd48d5 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 pom SEquence DAtaset builder @@ -41,18 +41,22 @@ Miguel Reboiro-Jato SING Group - University of Vigo http://www.sing-group.org - mrjato@uvigo.es + mrjato@uvigo.gal Hugo López-Fernández SING Group - University of Vigo http://www.sing-group.org - hlfernandez@uvigo.es + hlfernandez@uvigo.gal David Vila Fernández Escola Superior de Enxeñaría Informática - University of Vigo + + Miguel José da Silva Araújo + Escola Superior de Enxeñaría Informática - University of Vigo + @@ -86,7 +90,7 @@ 2.3.0-SNAPSHOT - 1.7.0-SNAPSHOT + 1.7.0 1.8.3 1.2.0 2.5.2 diff --git a/seda-distribution/resources/seda-cli-distributable-choices.xml b/seda-distribution/resources/seda-cli-distributable-choices.xml index 6b75b69..520ca68 100644 --- a/seda-distribution/resources/seda-cli-distributable-choices.xml +++ b/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 . diff --git a/seda-distribution/resources/seda-gui-distributable-choices.xml b/seda-distribution/resources/seda-gui-distributable-choices.xml index 4c03bdd..c50d16a 100644 --- a/seda-distribution/resources/seda-gui-distributable-choices.xml +++ b/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 . diff --git a/seda-docker/Dockerfile.local b/seda-docker/Dockerfile.local index b51c7fd..9c70fea 100644 --- a/seda-docker/Dockerfile.local +++ b/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 diff --git a/seda-docker/README.md b/seda-docker/README.md index ccd3163..b21af1b 100644 --- a/seda-docker/README.md +++ b/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 ` (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 ` (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 $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0-v2304 /opt/SEDA/run-cli.sh -if /data/input.fasta -od /data/output ` +You should adapt and run the following command: `docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh -if /data/input.fasta -od /data/output ` In this command, you should replace: - `/your/data/dir` to point to the directory that contains the input file you want to process with SEDA. @@ -30,4 +30,4 @@ In this command, you should replace: - `` to the SEDA command you want to execute. - `` to the list of command parameters. -For instance, in order to sort a FASTA file, you should run: `docker run --rm -ti -e USERID=$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` diff --git a/seda-docker/docker-compose.yml b/seda-docker/docker-compose.yml index 3bba064..837828d 100644 --- a/seda-docker/docker-compose.yml +++ b/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 diff --git a/seda-plugin-bedtools/pom.xml b/seda-plugin-bedtools/pom.xml index ce175c5..7f5c860 100644 --- a/seda-plugin-bedtools/pom.xml +++ b/seda-plugin-bedtools/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-blast/pom.xml b/seda-plugin-blast/pom.xml index a2ef307..a954876 100644 --- a/seda-plugin-blast/pom.xml +++ b/seda-plugin-blast/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-cga/pom.xml b/seda-plugin-cga/pom.xml index 524442c..81d5ab6 100644 --- a/seda-plugin-cga/pom.xml +++ b/seda-plugin-cga/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-clustalomega/pom.xml b/seda-plugin-clustalomega/pom.xml index 07db146..94fca90 100644 --- a/seda-plugin-clustalomega/pom.xml +++ b/seda-plugin-clustalomega/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-emboss/pom.xml b/seda-plugin-emboss/pom.xml index 906a170..80affec 100644 --- a/seda-plugin-emboss/pom.xml +++ b/seda-plugin-emboss/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-pfam/pom.xml b/seda-plugin-pfam/pom.xml index 8244554..12547cb 100644 --- a/seda-plugin-pfam/pom.xml +++ b/seda-plugin-pfam/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-prosplign-procompart/pom.xml b/seda-plugin-prosplign-procompart/pom.xml index 98afce2..30c9d85 100644 --- a/seda-plugin-prosplign-procompart/pom.xml +++ b/seda-plugin-prosplign-procompart/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-sapp/pom.xml b/seda-plugin-sapp/pom.xml index 2047444..41c572d 100644 --- a/seda-plugin-sapp/pom.xml +++ b/seda-plugin-sapp/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda-plugin-splign-compart/pom.xml b/seda-plugin-splign-compart/pom.xml index d51fc29..6f011f8 100644 --- a/seda-plugin-splign-compart/pom.xml +++ b/seda-plugin-splign-compart/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml diff --git a/seda/pom.xml b/seda/pom.xml index 5b7a692..45e7d2a 100644 --- a/seda/pom.xml +++ b/seda/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.6.0-SNAPSHOT + 1.6.0 ../pom.xml