Merge pull request #57 from hariszaf/ARMS

.gitignore

@@ -22,3 +22,6 @@ pema_docker_image/sanity_check/18S/
 pema_docker_image/sanity_check/COI/
 pema_docker_image/sanity_check/ITS/
 pema_docker_image/sanity_check/12S/
+
+# Ignore any .sif file
+*.sif

README.md

@@ -4,7 +4,7 @@
 
 
 # PEMA: 
-## a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes 
+### a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes 
 *PEMA is reposited in* [*Docker Hub*](https://hub.docker.com/r/hariszaf/pema) *as well as in* [*Singularity Hub*](https://singularity-hub.org/collections/2295)
 
 #### PEMA website along with *how to* documentation can be found [**here**](https://hariszaf.github.io/pema_documentation/).
@@ -20,10 +20,18 @@ Table of Contents
 =================
 
    * [PEMA: biodiversity in all its different levels](#pema-biodiversity-in-all-its-different-levels)
-   * [ A container-based tool](#a-container-based-tool)
-   * [How to run PEMA](#how-to-run-pema)
-      * [Parameters' file](#parameters-file)
-   * [PEMA on HPC](#pema-on-hpc)
+   * [A container-based tool](#a-container-based-tool)
+   * [How to run PEMA](#get-set-go-pema)
+      * [Get](#get)
+      * [Set](#set)
+      * [Go](#go)
+   * [The Parameters' file](#parameters-file)
+   * [Downstream ecological analysis](#downstream-ecological-analysis)
+   * [Acknowledgments](#acknowledgments)
+   * [License](#license)
+   * [Citation](#citation)
+
+<!--   * [PEMA on HPC](#pema-on-hpc)
       * [Prerequisites](#prerequisites-1)
       * [Installing](#installing-1)
       * [Running PEMA](#running-pema-1)
@@ -33,16 +41,7 @@ Table of Contents
       * [Installing](#installing)
       * [Running PEMA](#running-pema)
          * [Step 1 - Build a Docker container](#step-1---build-a-docker-container)
-         * [Step 2 - Run PEMA](#step-2---run-pema)
-   * [phyloseq - for a downstream ecological analysis](#the-phyloseq-r-package)
-   * [Acknowledgments](#acknowledgments)
-   * [License](#license)
-   * [Citation](#citation)
-
-
-```diff
-+ You may have a look on pema's main website: http://pema.hcmr.gr/
-```
+         * [Step 2 - Run PEMA](#step-2---run-pema) -->
 
 
 <!-- ![Anurag's GitHub stats](https://github-readme-stats.vercel.app/api?username=hariszaf&show_icons=true&theme=onedark) -->
@@ -105,8 +104,7 @@ PEMA runs either as a [**Docker**](https://www.docker.com/) or as a [**Singulari
 
 ### Get
 
-To get PEMA running you first need to make sure you either have  
-**[Singularity]( https://www.sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps )** , 
+To get PEMA running you first need to make sure you either have **[Singularity]( https://www.sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps )** , 
 or Docker on your computing environment. 
 
 In case you are working on Singularity, you may run the following command to get the PEMA Singularity image:
@@ -250,8 +248,7 @@ So, here is the [***parameters.tsv***](https://github.com/hariszaf/pema/blob/mas
 
 
 
-## The "phyloseq" R package 
-**for a downstream ecological analysis of OTUs/ASVs retrieved**
+## Downstream ecological analysis
 
 PEMA performs all the basic functions of the "phyloseq" R package. In addition, it performs certain functions of the [***vegan***](https://cran.r-project.org/web/packages/vegan/index.html) R package. 
 

Singularity

@@ -2,7 +2,7 @@
 
 # Set base image
 Bootstrap: docker
-From: hariszaf/pema:v.2.1.4
+From: hariszaf/pema:v.2.1.5-beta
 
 # Set Singularity environment
 %post

analysis_directory/README.md

@@ -6,3 +6,37 @@ and the `parameters.tsv` file.
 Please, remove the README.md file that you will find on the `mydata` directory. Raw data files must be included there **only**.
 
 Everything else on this directory is **optional**, depending on the parameters set you will choose.
+
+
+
+You only need this directory, in case you need to use your own reference database.
+
+If that is the case, **you need to keep the name of this directory exactly as it is**, i.e ```custom_ref_db```.
+
+
+In case of 16/18S and ITS you need to train the CREST algorithm with your custom reference database. 
+You may see the relative steps [here](https://hariszaf.github.io/pema_documentation/training_crest_classifier/).
+
+Likewise, for the case of the COI marker gene, you need to train the RDPClassifier and you may see how 
+[here](https://hariszaf.github.io/pema_documentation/training_rdpclassifier/).
+
+
+
+These two are example files for the case you need to train the RDPClassifier with your own reference database. 
+
+In this case, we had a list of species known to be present at Amvrakikos gulf, Greece. 
+
+We extracted all the relative sequences from Midori2 database to build the `taxonomy_file` and the `sequences_file` in the right format.
+
+
+**You need to provide PEMA** with two such files having the **exact format** as the ones here. 
+
+In any other case, PEMA will not be able to train the classiier with your reference database and it will return an error. 
+
+
+You may find more about how to build these files and train the RDPClassifier over 
+[here](https://hariszaf.github.io/pema_documentation/training_rdpclassifier/).
+
+
+
+