moving to v0.5.3

Author: trtcrd

README.md

@@ -12,7 +12,7 @@ See below for full instructions
 
 # Accessing the webserver
 
-The execution of the `start_slim_v0.5.2.sh` script deploys and start the webserver.
+The execution of the `start_slim_v0.5.3.sh` script deploys and start the webserver.
 By default, the webserver is accessible on the 8080 port.
 
 * To access it on a remote server from your machine, type the server IP address followed by ":8080" (for example `156.241.0.12:8080`) from an internet browser (prefer Firefox and Google Chrome).
@@ -149,12 +149,12 @@ First of all, docker needs to be installed on the machine. You can find instruct
 * [docker for Ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/)
 * [docker for macOS](https://docs.docker.com/docker-for-mac/install/)
 
-To install SLIM, get the last stable release [here](https://github.com/trtcrd/SLIM/archive/v0.5.2.tar.gz) or, using terminal :
+To install SLIM, get the last stable release [here](https://github.com/trtcrd/SLIM/archive/v0.5.3.tar.gz) or, using terminal :
 ```bash
 sudo apt-get update && apt-get install git curl
-curl -OL https://github.com/trtcrd/SLIM/archive/v0.5.2.tar.gz
-tar -xzvf v0.5.2.tar.gz
-cd SLIM-0.5.2
+curl -OL https://github.com/trtcrd/SLIM/archive/v0.5.3.tar.gz
+tar -xzvf v0.5.3.tar.gz
+cd SLIM-0.5.3
 ```
 
 Before deploying SLIM, you need to configure the mailing account that will be used for mailing service.
@@ -174,13 +174,13 @@ exports.mailer = {
 ```
 
 
-As soon as docker is installed and running, the SLIM archive downloaded and the mailing account set, it can be deployed by using the two scripts `get_dependencies_slim_v0.5.2.sh` and `start_slim_v0.5.2.sh` as **super user**.
-* `get_dependencies_slim_v0.5.2.sh` fetches all the bioinformatics tools needed from their respective repositories.
-* `start_slim_v0.5.2.sh` destroys the current running webserver to replace it with a new one. **/!\\** All the files previously uploaded and the results of analysis will be detroyed during the process.
+As soon as docker is installed and running, the SLIM archive downloaded and the mailing account set, it can be deployed by using the two scripts `get_dependencies_slim_v0.5.3.sh` and `start_slim_v0.5.3.sh` as **super user**.
+* `get_dependencies_slim_v0.5.3.sh` fetches all the bioinformatics tools needed from their respective repositories.
+* `start_slim_v0.5.3.sh` destroys the current running webserver to replace it with a new one. **/!\\** All the files previously uploaded and the results of analysis will be detroyed during the process.
 
 ```bash
-sudo bash get_dependencies_slim_v0.5.2.sh
-sudo bash start_slim_v0.5.2.sh
+sudo bash get_dependencies_slim_v0.5.3.sh
+sudo bash start_slim_v0.5.3.sh
 ```
 
 The server is configured to use up to 8 CPU cores per job. The amount of available cores will determine the amount of job that can be executed in parallel (1-8 -> 1 job, 16 -> 2 jobs, etc.). To admin and access SLIM logs, please refer to the docker command line [documentation](https://docs.docker.com/engine/reference/commandline/docker/).
@@ -219,34 +219,38 @@ Please refer to the wiki pages to learn [how to create a module](https://github.
 
 # Version history
 
-v0.5.2
+### v0.5.3
+
+DTD: added an option for trimming the primers at the end of the reads in and a length filtering (primers dimers issue)
+
+### v0.5.2
 
 DADA2 beta integration, small fix on IDATAXA
 
-v0.5.1
+### v0.5.1
 
 BUGFIX of the IDTAXA module, added wiki for the module
 
-v0.5
+### v0.5
 
 Integration of the IDTAXA module
 
-v0.4.1
+### v0.4.1
 
 Fixed the Dockerfile to fetch the latest R version and CASPER util.c file
 
-v0.4
+### v0.4
 
 Added timing checkpoints in the logs of the scheduler; Added the third-party software version infos in the email
 
-v0.3
+### v0.3
 
 Fixed LULU module and the otu table writing is now done by a python script
 
-v0.2
+### v0.2
 
 Updated the `get_dependencies` script.
 
-v0.1
+### v0.1
 
 First release, with third-parties versions handled within the `get_dependencies_slim.sh` script.

get_dependencies_slim_v0.5.2.sh get_dependencies_slim_v0.5.3.sh

@@ -1,4 +1,4 @@
-### SLIM v0.5.2 ###
+### SLIM v0.5.3 ###
 #Third-party software version:
 casper		0.8.2
 DTD		0.1