Merge pull request #14 from NIGMS/AWS-GCP

AWS + Google Cloud

Author: kyleoconnell-NIH

AWS/01-RNA-Seq/RNA-seq.ipynb

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Create a conda environment
+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-rna-seq
+
+# Install packages
+conda install -c conda-forge -c bioconda bioconductor-deseq2 -y
+
+conda install r-hexbin -y
+
+conda install conda-forge::r-tidyverse -y
+
+conda install bioconda::bioconductor-bsgenome -y
+
+conda install bioconda::bioconductor-vsn -y 
+
+conda install bioconda::bioconductor-genomation -y
+
+conda install bioconda::bioconductor-genomeinfodb -y
+
+R -e 'install.packages(c("NMF","IRkernel"), repos="http://cran.rstudio.com/")'
+
+
+# Install the kernel specification for Jupyter
+R -e 'IRkernel::installspec(name = "R-RNA-Seq", displayname = "R-RNA-Seq")' 

AWS/01-RNA-Seq/install_rna_seq_packages.sh

@@ -0,0 +1,21 @@
+plugins {
+    id 'nf-amazon'
+}
+
+profiles {
+    aws {
+        process {
+            executor = 'awsbatch'
+            queue = 'nextflow-batch-job-queue'  // Name of your Job queue
+            container = 'quay.io/nextflow/rnaseq-nf:v1.1'
+            
+        }
+        workDir = 's3://your_bucket_name/rna-tmp/'    // path of your working directory
+        params.outdir = 's3://your_bucket_name/rna-outputs/'   // path of your output directory
+        
+        fusion.enabled = true
+        wave.enabled = true
+        aws.region = 'us-east-1' // YOUR AWS REGION
+
+    }
+}

AWS/01-RNA-Seq/rnaseq-aws.config

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Create a conda environment
+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-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
+
+conda install bioconda::bioconductor-genomation -y
+
+conda install conda-forge::r-ggforce -y
+
+conda install conda-forge::r-tidyverse -y
+
+R -e 'install.packages(c("IRkernel","ggplot2"), repos="http://cran.rstudio.com/")'
+
+# Install the kernel specification for Jupyter
+R -e 'IRkernel::installspec(name = "R-RRBS", displayname = "R-RRBS")' 

AWS/02-RRBS/RRBS-downstream.ipynb

@@ -0,0 +1,21 @@
+plugins {
+    id 'nf-amazon'
+}
+
+profiles {
+    aws {
+        process {
+            executor = 'awsbatch'   
+            queue = 'nextflow-batch-job-queue' // Name of your Job queue
+            container = 'quay.io/nextflow/rnaseq-nf:v1.1'
+            
+        }
+        workDir = 's3://nextflow-bucket-test/meth-tmp/'   // Path of your working directory
+        params.outdir = 's3://nextflow-bucket-test/meth-outputs/'   // Path of your output directory
+        
+        fusion.enabled = true
+        wave.enabled = true
+        aws.region = 'us-east-1' // YOUR AWS REGION
+
+    }
+}

AWS/02-RRBS/install_rrbs_packages.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Create a conda environment
+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-integration
+
+# Install packages
+
+conda install conda-forge::r-pvclust -y
+
+conda install conda-forge::r-ggnewscale -y 
+
+conda install conda-forge::r-ggridges -y
+
+conda install conda-forge::r-europepmc -y
+
+conda install conda-forge::r-ggseqlogo -y
+
+conda install bioconda::bioconductor-methreg -y
+
+conda install bioconda::bioconductor-bsgenome -y
+
+conda install bioconda::bioconductor-clusterprofiler -y
+
+conda install bioconda::bioconductor-pathview -y
+
+conda install bioconda::bioconductor-enrichplot -y
+
+conda install bioconda::bioconductor-repitools -y
+
+conda install bioconda::bioconductor-rnaagecalc -y 
+
+conda install bioconda::bioconductor-motifmatchr -y
+
+conda install bioconda::bioconductor-tfbstools -y 
+
+conda install conda-forge::r-doparallel -y
+
+conda install bioconda::bioconductor-bsgenome.hsapiens.ucsc.hg38 -y
+
+conda install -c conda-forge r-data.table=1.16.4 -y
+conda install bioconda::bioconductor-methylkit -y
+
+conda install bioconda::bioconductor-genomation -y
+
+conda install bioconda::bioconductor-deseq2 -y
+
+conda install conda-forge::r-tidyverse -y
+
+conda install bioconda::bioconductor-motifstack -y
+
+
+
+R -e 'install.packages(c("IRkernel"), repos="http://cran.rstudio.com/")'
+
+# Install the kernel specification for Jupyter
+R -e 'IRkernel::installspec(name = "R-Integration", displayname = "R-Integration")'