Commit cab5ac5b authored by jlopez's avatar jlopez
Browse files

Fix workflows

parent 67e65134
......@@ -107,7 +107,7 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
size <- length(data)
intalls <- ""
res <- ""
res <- c()
for (tools in data) {
splitB <- strsplit(tool, "%")
......@@ -118,11 +118,10 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
if(tools$version == version) {
for (c in tools$dependencies) {
tt <- paste0(c$name, "%", c$version)
print(tt)
res <- paste0(res, getInstallToolPackageBioContainer(tt, containerType))
res <- paste0(res, "\n")
res <- c(res, getInstallToolPackageBioContainer(tt, containerType))
}
res <- paste0(res, "\t", tools$install, collapse='\n' )
res <- c(res, paste0("\t", tools$install, collapse='\n' ))
print(res)
return(res)
}
}
......@@ -150,7 +149,7 @@ getInstallToolPackageBioContainer <- function(tool, containerType) {
res <- paste0("\t", tools$install, collapse='\n' )
res <- paste0("\t", tools$install, collapse='\n' )
return(res)
}
}
......
......@@ -517,13 +517,16 @@ createWorkflows <- function(result, haveR, haveConda) {
for (tool in selectWorkflows){
result <- paste(result, '############### Install Workflow tools ##############', sep = "\n")
result <- paste(result, '############### Install Workflow tools ##############\n', sep = "\n")
result <- paste(result, getInstallToolPackageWorkflow(tool, input$containerType), sep="\n\n")
for(i in getInstallToolPackageWorkflow(tool, input$containerType)) {
result <- paste0(result, i, "\n")
}
}
} else {
selectBioTool <- input$selectedBiocontainer
selectWorkflows <- input$selectedWorkflows
result <- paste0(result, "\n")
......@@ -573,12 +576,13 @@ createWorkflows <- function(result, haveR, haveConda) {
result <- paste(result, "RUN chmod 777 -R /opt/workflows/", sep = "\n")
result <- paste(result, "ENV PATH=/opt/workflows/bin:${PATH}", sep = "\n")
for (tool in selectBioTool){
result <- paste(result, '############### Install Workflow ##############', sep = "\n")
for (tool in selectWorkflows){
result <- paste(result, '############### Install Workflow ##############\n', sep = "\n")
result <- paste0(result, "\nRUN ", getInstallToolPackageWorkflow(tool, input$containerType))
for(i in getInstallToolPackageWorkflow(tool, input$containerType)) {
result <- paste0(result, "RUN", i, "\n")
}
}
}
......@@ -635,7 +639,7 @@ createBiocontainer <- function(result, haveR) {
for (tool in selectBioTool){
result <- paste(result, '############### Install BioContainer tools ##############', sep = "\n")
result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
result <- paste(result, getInstallToolPackageBioContainer(tool, input$containerType), sep="\n\n")
......@@ -684,10 +688,10 @@ createBiocontainer <- function(result, haveR) {
for (tool in selectBioTool){
result <- paste(result, '############### Install BioContainer tools ##############', sep = "\n")
result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
result <- paste0(result, "\nRUN ", getInstallToolPackageBioContainer(tool, input$containerType))
result <- paste0(result, "RUN ", getInstallToolPackageBioContainer(tool, input$containerType))
}
}
......
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