change environment and project name to GEP

README.md

-# Genome Evaluation with Snakemake
+# Genome Evaluation Pipeline
 
 This pipeline allows users the ability to produce a wide range of commonly used evaluation metrics for genome assemblies, no matter your level of command-line experience/.
 
@@ -103,17 +103,17 @@ source ~/.bashrc
 
 **Step 3. Creating our Snakemake conda environment**
 - 
-Inside the main porject folder will be a file called `installEnvironment.yaml`
+Inside the main porject folder will be a file called `installGEP.yaml`
 
 i.e.
-`/<your_path_to>/genome_evaluation_snakemake/installEnvironment.yaml`
+`/<your_path_to>/GEP/installGEP.yaml`
 
 If you have followed the process of installing miniconda3 correctly (along with closing and
-re-opening your terminal or sourcing your bash profile), installing your snakemake environment is very simple.
+re-opening your terminal or sourcing your bash profile), installing your GEP environment is very simple.
 
-To create/install snakemake environment:
+To create/install GEP environment:
 ```
-conda env create -f installEnvironment.yaml
+conda env create -f installGEP.yaml
 ```
 
 The environment should install on it's own, press ENTER if prompted to install the list of
@@ -121,7 +121,7 @@ packages.
 
 Your environment is now created and installed - we want to activate it by running the command:
 ```
-conda activate snakemake
+conda activate GEP
 ```
 
 
@@ -167,9 +167,9 @@ Secondly, we will modify the `config.yaml` which will look like this:
 ```
 ##Configuration files pathways
 
-Results: "/path/to/desiredDestination/Results_AssemblyEval"
+Results: "/<PathTo>/desiredDestination/Results_AssemblyEval"
 
-samplesTSV: "/path/to/configuration/samples.tsv"
+samplesTSV: "/<PathTo>/GEP/configuration/samples.tsv"
 
 busco4Lineage: "vertebrata"
 
@@ -186,7 +186,7 @@ This is the path to the aforemention `samples.tsv` that was created/modified jus
 3. `busco4Lineage` Busco needs a database to be able to run.  Here you have a couple of different options.
  - Manually download and unpack your desired database from https://busco-data.ezlab.org/v4/data/lineages/ . In this case (or if you already have the database downloaded to a specific location), you can provide the full path: 
 ```
-busco4Lineage: "/path/to/manually/Downloaded/vertebrata_odb10"
+busco4Lineage: "/<PathTo>/manuallyDownloaded/vertebrata_odb10"
 ```
 
  - Alternatively, you can just provide the taxonomy name that you wish to use. In this case, the latest database matching the name provided will be automatically downloaded prior to execution, if it doesn't already exist inside the `buscoLineage` directory. If it already exists in this `buscoLineage` either from manual download or from previously automatic download (from previously executed runs), then the pipeline will skip re-downloading.
@@ -203,9 +203,9 @@ If everything is set up correctly, we can run the pipeline very simply.
 
 For now (though it should be a simple fix!), you must run the pipeline while being inside the project folder.  In otherwords, you must be inside the folder where the file `Snakefile` is directly accessible. 
 
-*Make sure your snakemake environment is activated.*
+*Make sure your GEP environment is activated.*
 
-First you should run snakemake in drymode:
+First you should run GEP in drymode:
 
 ```
 snakemake -n

installEnvironment.yaml → installGEP.yaml

-name: snakemake
+name: GEP
 channels:
  - conda-forge
  - bioconda