rbbt-util 5.26.50 → 5.26.52

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6ad025ffbbc79d8356f9e916655618371fe9abd5b895f3eee8bd387eb89ff424
-  data.tar.gz: 3981bc550db7b77d336dc012a61790a9888db0d7c33cd1f1f9f126bc15faedec
+  metadata.gz: a0c1ab4c13e21adcf7fc03ca763cd2430d559fef8308bcdeaa1c0d1e1f024a93
+  data.tar.gz: e6703b4fbdbc3b32bd06a545dbaed2f73543b59ed6818edf35aa8ac321f474c8
 SHA512:
-  metadata.gz: 1bafe260c48058be8ac2ae664198ce3c3b6b98a9d3eadbc5dca3783d3fd29fac81031691898d4beccfc1328a54f93247cee93be9aff36212efa93c1cab91c3fa
-  data.tar.gz: ea29321785787aa70a2e8f02c3c07f23175aff29c4f3f3d2421605b5820a9502cdad1adcf959fc0548b41e2f356fe147437e78eb273bce8012653f6c311de133
+  metadata.gz: 1e3a4ae83c95e42cb51722bf9b155a52ab116ea072fbe26ab0f8133a416efc8e803e2710e4e8b4bc36332471f7bbd489c7927a532f9c2d350380b96b9ccc3eb8
+  data.tar.gz: 2bb689e5a847d74cf537c52e11a062d96229ac2d948f346ee2131493ae5f135a372dfc780b6e3ae3033298087a2e930c0950b972df3f4ee27d7714fd02a4a497

data/lib/rbbt/workflow/accessor.rb

@@ -441,6 +441,7 @@ class Step
   def dirty?
     return true if Open.exists?(pid_file) && ! ( Open.exists?(info_file) || done? )
     return false unless done? || status == :done
+    return false unless ENV["RBBT_UPDATE"] == "true"
 
     status = self.status
 

data/lib/rbbt/workflow/step/dependencies.rb

@@ -93,6 +93,7 @@ class Step
           (!(job.noinfo? || job.done? || job.error? || job.aborted? || job.running?))
 
         job.clean 
+        job.set_info :status, :cleaned
       end
 
       job.dup_inputs unless status == 'done' or job.started?

data/lib/rbbt/workflow/step/run.rb

@@ -179,6 +179,7 @@ class Step
   end
 
   def updated?
+    return true if ENV["RBBT_UPDATE"] != "true"
     return true unless (done? || error? || ! writable?)
 
     @updated ||= out_of_date.empty?

data/share/Rlib/util.R

@@ -1,5 +1,5 @@
 rbbt.ruby.exec.singularity <- function(code, image){
-  return(system(paste('singularity -e exec', image,'rbbt_exec.rb - file', sep=" "), input = code, intern=TRUE));
+  return(system(paste('singularity -e exec "', image,'" rbbt_exec.rb - file', sep=""), input = code, intern=TRUE));
 }
 
 rbbt.ruby.exec <- function(code){

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.50
+  version: 5.26.52
 platform: ruby
 authors:
 - Miguel Vazquez