From cab5ac5b9e572a2f03f1e3ee17fab5f0ac4ac220 Mon Sep 17 00:00:00 2001
From: jlopez <jimmy.lopez0023@gmail.com>
Date: Tue, 27 Nov 2018 16:16:43 +0100
Subject: [PATCH] Fix workflows
---
R/helper_functions.R | 11 +++++------
server/opt_home.R | 24 ++++++++++++++----------
2 files changed, 19 insertions(+), 16 deletions(-)
diff --git a/R/helper_functions.R b/R/helper_functions.R
index d94bc7b..975e31d 100644
--- a/R/helper_functions.R
+++ b/R/helper_functions.R
@@ -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)
}
}
diff --git a/server/opt_home.R b/server/opt_home.R
index 9a02346..4ceca3f 100755
--- a/server/opt_home.R
+++ b/server/opt_home.R
@@ -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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