address review feedback (#232)

* address review feedback

* add reference to github and bioconductor packages in worker

* update package management sample

docs/20-package-management.md

@@ -8,7 +8,7 @@ Packages installed at the pool level benefit from only needing to be installed o
 
 ## Installing Packages on Pool Creation
 
-Pool level packages support CRAN, GitHub and BioConductor packages. The packages are installed in a shared directory on the node. It is important to note that it is required to explicitly load any packages installed at the cluster level within the foreach loop. For example, if you installed xml2 on the cluster, you must explicityly load it before using it.
+Pool level packages support CRAN, GitHub and BioConductor packages. The packages are installed in a shared directory on the node. It is important to note that it is required to explicitly load any packages installed at the cluster level within the foreach loop. For example, if you installed xml2 on the cluster, you must explicitly load it before using it.
 
 ```R
 foreach (i = 1:4) %dopar% {

inst/startup/worker.R

@@ -83,6 +83,14 @@ for (package in azbatchenv$packages) {
   library(package, character.only = TRUE)
 }
 
+for (package in azbatchenv$github) {
+  library(package, character.only = TRUE)
+}
+
+for (package in azbatchenv$bioconductor) {
+  library(package, character.only = TRUE)
+}
+
 ls(azbatchenv)
 parent.env(azbatchenv$exportenv) <- getparentenv(azbatchenv$pkgName)
 

samples/package_management/bioconductor.r

@@ -1,3 +1,5 @@
+#Please see documentation at docs/20-package-management.md for more details on packagement management.
+
 # install packages
 library(devtools)
 install_github("azure/doazureparallel")
@@ -6,24 +8,30 @@ install_github("azure/doazureparallel")
 library(doAzureParallel)
 
 # set your credentials
-setCredentials("credentials.json")
+doAzureParallel::setCredentials("credentials.json")
 
 # Create your cluster if not exist
-cluster <- makeCluster("bioconductor_cluster.json")
+cluster <- doAzureParallel::makeCluster("bioconductor_cluster.json")
 
 # register your parallel backend
-registerDoAzureParallel(cluster)
+doAzureParallel::registerDoAzureParallel(cluster)
 
 # check that your workers are up
-getDoParWorkers()
+doAzureParallel::getDoParWorkers()
 
 summary <- foreach(i = 1:1) %dopar% {
   library(GenomeInfoDb) # Already installed as part of the cluster configuration
   library(IRanges) # Already installed as part of the cluster configuration
 
   sessionInfo()
   # Your algorithm
+}
+
+summary
 
+summary <- foreach(i = 1:1, bioconductor=c('GenomeInfoDb', 'IRanges')) %dopar% {
+  sessionInfo()
+  # Your algorithm
 }
 
 summary