Simplify templates

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9947
+Version: 0.12.2-9948
 Depends:
     R (>= 3.2.0),
     parallelly,

R/batchtools_sge.R

@@ -40,8 +40,12 @@ BatchtoolsSGEFutureBackend <- function(...) {
 #' @examplesIf interactive()
 #' library(future)
 #'
-#' # Limit runtime to 3 minutes and memory to 200 MiB per future
-#' plan(future.batchtools::batchtools_sge, resources = list(h_rt = "00:03:00", mem_free = "200M"))
+#' # Limit runtime to 3 minutes and memory to 200 MiB per future,
+#' # request two slots and run in the current working directory.
+#' plan(future.batchtools::batchtools_sge, resources = list(
+#'   h_rt = "00:03:00", mem_free = "200M",
+#'   asis = c("-pe smp 2", "-cwd")
+#' ))
 #'
 #' f <- future(Sys.info())
 #' info <- value(f)

inst/templates/lsf.tmpl

@@ -13,18 +13,19 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
-  prefix <- "#BSUB "
-    
   ## As-is resource specifications
   if ("asis" %in% names(resources)) {
-    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    lines <- resources[["asis"]]
     resources <- resources[names(resources) != "asis"]
+  } else {
+    lines <- character(0)
   }
 
   ## Remaining resources are assumed to be of type '-<key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  writeLines(sprintf("%s%s", prefix, opts))
+  lines <- sprintf("#BSUB %s", c(lines, opts))
+  writeLines(lines)
 } %>
 
 echo "Batchtools information:"
@@ -42,7 +43,7 @@ echo
 
 echo "Job submission declarations:"
 <%
-  writeLines(sprintf("echo '#BSUB %s'", opts))
+  writeLines(sprintf("echo '%s'", lines))
 %>
 
 echo "Job information:"

inst/templates/openlava.tmpl

@@ -13,18 +13,19 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
-  prefix <- "#BSUB "
-    
   ## As-is resource specifications
   if ("asis" %in% names(resources)) {
-    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    lines <- resources[["asis"]]
     resources <- resources[names(resources) != "asis"]
+  } else {
+    lines <- character(0)
   }
 
   ## Remaining resources are assumed to be of type '-<key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  writeLines(sprintf("%s%s", prefix, opts))
+  lines <- sprintf("#BSUB %s", c(lines, opts))
+  writeLines(lines)
 } %>
 
 echo "Batchtools information:"
@@ -42,7 +43,7 @@ echo
 
 echo "Job submission declarations:"
 <%
-  writeLines(sprintf("echo '#BSUB %s'", opts))
+  writeLines(sprintf("echo '%s'", lines))
 %>
 
 echo "Job information:"

inst/templates/sge.tmpl

@@ -25,21 +25,19 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
-  prefix <- "#$ "
-    
-  ## As-is resource specifications, e.g.
-  ## sge_options <- c("-pe smp 2", "-R yes")
-  ## plan(batchtools_sge, resources = list(asis = sge_options))
+  ## As-is resource specifications
   if ("asis" %in% names(resources)) {
-    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    lines <- resources[["asis"]]
     resources <- resources[names(resources) != "asis"]
+  } else {
+    lines <- character(0)
   }
-
-  ## Remaining resources are assumed to be of type '-l <key>=<value>', e.g.
-  ## plan(batchtools_sge, resources = list(mem_free = "1G", h_rt="00:20:00"))
+     
+  ## Remaining resources are assumed to be of type '-l <key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-l %s=%s", names(opts), opts)
-  writeLines(sprintf("%s%s", prefix, opts))
+  lines <- sprintf("#$ %s", c(lines, opts))
+  writeLines(lines)
 } %>
 
 echo "Batchtools information:"
@@ -57,7 +55,7 @@ echo
 
 echo "Job submission declarations:"
 <%
-writeLines(sprintf("echo '#$ %s'", opts))
+  writeLines(sprintf("echo '%s'", lines))
 %>
 
 echo "Job information:"

inst/templates/slurm.tmpl

@@ -11,18 +11,19 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
-  prefix <- "#SBATCH "
-    
   ## As-is resource specifications
   if ("asis" %in% names(resources)) {
-    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    lines <- resources[["asis"]]
     resources <- resources[names(resources) != "asis"]
+  } else {
+    lines <- character(0)
   }
-
+     
   ## Remaining resources are assumed to be of type '--<key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("--%s=%s", names(opts), opts)
-  writeLines(sprintf("%s%s", prefix, opts))
+  lines <- sprintf("#SBATCH %s", c(lines, opts))
+  writeLines(lines)
 } %>
 
 echo "Batchtools information:"
@@ -40,7 +41,7 @@ echo
 
 echo "Job submission declarations:"
 <%
-writeLines(sprintf("echo '#SBATCH %s'", opts))
+  writeLines(sprintf("echo '%s'", lines))
 %>
 
 echo "Slurm job information:"

inst/templates/torque.tmpl

@@ -19,18 +19,19 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
-  prefix <- "#PBS "
-    
   ## As-is resource specifications
   if ("asis" %in% names(resources)) {
-    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    lines <- resources[["asis"]]
     resources <- resources[names(resources) != "asis"]
+  } else {
+    lines <- character(0)
   }
 
   ## Remaining resources are assumed to be of type '-l <key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-l %s=%s", names(opts), opts)
-  writeLines(sprintf("%s%s", prefix, opts))
+  lines <- sprintf("#PBS %s", c(lines, opts))
+  writeLines(lines)
 } %>
 
 echo "Batchtools information:"
@@ -48,7 +49,7 @@ echo
 
 echo "Job submission declarations:"
 <%
-  writeLines(sprintf("echo '#PBS -l %s'", opts))
+  writeLines(sprintf("echo '%s'", lines))
 %>
 
 echo "Job information:"