Moving to v0.4.1

Author: trtcrd

README.md

@@ -12,7 +12,7 @@ See below for full instructions
 
 # Accessing the webserver
 
-The execution of the `start_slim_v0.4.sh` script deploys and start the webserver.
+The execution of the `start_slim_v0.4.1.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).
@@ -63,8 +63,8 @@ ACTACTYCAAATCGG
 
 This FASTA file contains reference sequences with unique identifier and taxonomic path in the header.
 Such database can be downloaded for instance from [SILVA](https://www.arb-silva.de/) for both prokaryotes and eukaryotes (16S and 18S), [EUKREF](https://eukref.org/) or [PR2](https://github.com/pr2database/pr2database) for eukaryotes (18S), [UNITE](https://unite.ut.ee/repository.php) for fungi (ITS), [MIDORI](http://www.reference-midori.info/download.php#) for metazoan (COI).
-Each header include a unique identifier (usually the accession),  
-a space ' ', and the taxonomic path separated by a semi-colon (without any space, please use "_" underscore).  
+Each header include a unique identifier (usually the accession),
+a space ' ', and the taxonomic path separated by a semi-colon (without any space, please use "_" underscore).
 **You should have the same amount of taxonomic rank for each reference sequences**
 
 ```
@@ -136,9 +136,9 @@ Your files will remain available on the server during 24h, after what they will
 Each module status is displayed besides its names:
 - waiting: the execution started, the module is waiting for files input.
 - running: the module is busy.
-- warnings: there was some warnings during the execution, but the module is still running. 
-- aborted: the module aborted and the pipeline has stopped its execution. 
-- ended: the module has finnished its task. 
+- warnings: there was some warnings during the execution, but the module is still running.
+- aborted: the module aborted and the pipeline has stopped its execution.
+- ended: the module has finnished its task.
 
 For more details on the app, you can refer to the [wiki pages](https://github.com/yoann-dufresne/SLIM/wiki)
 
@@ -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/v0.4.tar.gz) or, using terminal :
+To install SLIM, get the last stable release [here](https://github.com/trtcrd/SLIM/archive/v0.4.1.tar.gz) or, using terminal :
 ```bash
 sudo apt-get update && apt-get install git curl
-curl -OL https://github.com/trtcrd/SLIM/archive/v0.4.tar.gz
-tar -xzvf v0.4.tar.gz
-cd SLIM-0.4
+curl -OL https://github.com/trtcrd/SLIM/archive/v0.4.1.tar.gz
+tar -xzvf v0.4.1.tar.gz
+cd SLIM-0.4.1
 ```
 
 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_v0.4.sh` and `start_slim_v0.4.sh` as **super user**.
-* `get_dependencies_slim_v0.4.sh` fetches all the bioinformatics tools needed from their respective repositories.
-* `start_slim_v0.4.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_v0.4.1.sh` and `start_slim_v0.4.1.sh` as **super user**.
+* `get_dependencies_slim_v0.4.1.sh` fetches all the bioinformatics tools needed from their respective repositories.
+* `start_slim_v0.4.1.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_v0.4.sh
-sudo bash start_slim_v0.4.sh
+sudo bash get_dependencies_slim_v0.4.1.sh
+sudo bash start_slim_v0.4.1.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/). 
@@ -217,9 +217,13 @@ Please refer to the wiki pages to learn [how to create a module](https://github.
 
 # Version history
 
+v0.4.1
+
+Fixed the Dockerfile to fetch the latest R version and CASPER util.c file
+
 v0.4
 
-Added timing checkpoints in the logs of the scheduler; Added the third-party software version infos in the email 
+Added timing checkpoints in the logs of the scheduler; Added the third-party software version infos in the email
 
 v0.3