updated package installations for submodule 1,2,3

Author: hadiparsianNIH

AWS/01-RNA-Seq/install_rna_seq_packages.sh

@@ -1,15 +1,13 @@
 #!/bin/bash
 
-conda update -n base -c defaults conda -y
-
 # Create a conda environment
-conda create -n r-package-1 -y
+conda create -n r-rna-seq r-base=4.3.3 -y
 
 # Consider addressing your conda initialization instead.
 source ~/.bashrc
 
 # Activate the Conda Environment
-conda activate r-package-1
+conda activate r-rna-seq
 
 # Install packages
 conda install -c conda-forge -c bioconda bioconductor-deseq2 -y

AWS/02-RRBS/install_rrbs_packages.sh

@@ -1,15 +1,16 @@
 #!/bin/bash
 
 # Create a conda environment
-conda create -n r-package-2 r-base=4.2.2 -y
+conda create -n r-rrbs r-base=4.3.3 -y
 
 # Consider addressing your conda initialization instead.
 source ~/.bashrc
 
 # Activate the Conda Environment
-conda activate r-package-2
+conda activate r-rrbs
 
 # Install packages
+conda install -c conda-forge r-data.table=1.16.4 -y
 conda install bioconda::bioconductor-methylkit -y
 
 conda install bioconda::bioconductor-genomicranges -y

AWS/03-Integration/install_integration_packages.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # Create a conda environment
-conda create -n r-package-3 r-base=4.3.3 -y
+conda create -n r-integration r-base=4.3.3 -y
 
 # Consider addressing your conda initialization instead
 source ~/.bashrc
 
 # Activate the Conda Environment
-conda activate r-package-3
+conda activate r-integration
 
 # Install packages