better installation with install.sh script

README.md

@@ -24,24 +24,10 @@ While the design of custom probes against bacterial or viral genomes is an excit
 
 **gene2probe** builds on many awesome bioinformatic tools that need to be preinstalled. Luckily, they should all be easy to install via conda/pip.
 
-We recommend setting up a dedicated conda environment.
+We recommend setting up a dedicated conda environment. If conda is already installed, the install.sh script will create the env, install support packages, and activate the env. 
 
 ```
-conda create -n gene2probe_env python=3.11
-```
-
-Install bedtools and blast
-
-```
-conda activate gene2probe_env
-conda install bioconda::blast
-conda install bioconda::bedtools
-```
-
-Then install gene2probe via pip
-
-```
-pip install git+https://github.com/Teichlab/gene2probe.git
+source install.sh
 ```
 
 ## Probe design recommendations and main principle

install.sh

@@ -0,0 +1,27 @@
+NEW_ENV="gene2probe_env"
+conda create -y -n $NEW_ENV python=3.11
+
+# Packages to install
+conda_forge_bioconda_packages=(
+    "ipython"
+    "nb_conda_kernels"
+)
+
+pip_packages=(
+    "biopython"
+)
+
+# Install packages from conda-forge or bioconda
+mamba install -y -n $NEW_ENV -c conda-forge -c bioconda "${conda_forge_bioconda_packages[@]}"
+
+# Install packages from pypi
+mamba run -y -n $NEW_ENV pip install "${pip_packages[@]}"
+mamba run -y -n $NEW_ENV conda install bioconda::bedtools
+mamba run -y -n $NEW_ENV conda install bioconda::blast
+
+
+#other installations
+conda run -n $NEW_ENV pip install git+https://github.com/Teichlab/gene2probe.git 
+
+conda activate $NEW_ENV
+