Updated peak_call yaml & jobs. Fixed r_spp wrapper to handle bad argparsing. ...

Updated peak_call yaml & jobs.  Fixed r_spp wrapper to handle bad argparsing.  Updated conf to include list of system commands.

chipathlon/conf.py

@@ -10,6 +10,18 @@ job_wrappers = "jobs/wrappers/"
 # Job scripts directory
 job_scripts = "jobs/scripts/"
 
+# SYSTEM PATH, probably /bin
+system_path = "/bin/"
+
+# System commands mv, cp, sort, zcat, awk e.t.c
+system_commands = [
+    "mv",
+    "cp",
+    "sort",
+    "zcat",
+    "awk"
+]
+
 # File extensions
 file_extensions = {
     "genome_index": ["fa", "fna"],

chipathlon/jobs/modules/peak_call.yaml

 peak_call:
   - spp[tool]:
-    - mv_bed_tagalign:
+    - cp_bed_tagalign:
         inputs:
           - exp.bed:
               type: file
@@ -8,7 +8,7 @@ peak_call:
         outputs:
           - exp.tagAlign:
               type: file
-    - mv_bed_tagalign:
+    - cp_bed_tagalign:
         inputs:
           - control.bed:
               type: file

chipathlon/jobs/params/mv_bed_tagalign.yaml → chipathlon/jobs/params/cp_bed_tagalign.yaml

-mv_bed_tagalign:
+cp_bed_tagalign:
   inputs:
     - bed:
         type: file
@@ -6,7 +6,7 @@ mv_bed_tagalign:
   outputs:
     - bed:
         type: file
-  command: mv_bed_tagalign.sh
+  command: cp
   arguments:
     - "$inputs.0":
         changeable: false

chipathlon/jobs/scripts/mv_bed_tagalign.sh

-#!/bin/bash
-
-/bin/mv "$1" "$2"

chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh

@@ -2,4 +2,11 @@
 
 . /util/opt/lmod/lmod/init/profile
 module load R spp
-Rscript ${SPP_NODUPS} "$@"
+newargs=()
+while (( ${#@} ))
+do
+    newargs+=("$1=$2")
+    shift
+    shift
+done
+Rscript ${SPP_NODUPS} "${newargs[@]/#/}"

chipathlon/workflow.py

@@ -107,6 +107,13 @@ class Workflow(object):
                 if self.debug:
                     print "[LOAD_EXECUTABLE] %s" % (f,)
             break
+        # Handle necessary installed scripts
+        for cmd in chipathlon.conf.system_commands:
+            self.executables[cmd] = Executable(name=cmd, os=os_type, arch=arch)
+            self.executables[cmd].addPFN(PFN("file://%s/%s" % (chipathlon.conf.system_path, cmd), "local"))
+            self.dax.addExecutable(self.executables[cmd])
+            if self.debug:
+                print "[LOAD_EXECUTABLE] %s" % (cmd,)
         # Overwrite pegasus::transfer to request more walltime
         """
         if self.config["profile"]["env"]["PEGASUS_HOME"]: