Commit 99c8ab3a authored by aknecht2's avatar aknecht2
Browse files

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.
parent a5561568
...@@ -10,6 +10,18 @@ job_wrappers = "jobs/wrappers/" ...@@ -10,6 +10,18 @@ job_wrappers = "jobs/wrappers/"
# Job scripts directory # Job scripts directory
job_scripts = "jobs/scripts/" 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
file_extensions = { file_extensions = {
"genome_index": ["fa", "fna"], "genome_index": ["fa", "fna"],
......
peak_call: peak_call:
- spp[tool]: - spp[tool]:
- mv_bed_tagalign: - cp_bed_tagalign:
inputs: inputs:
- exp.bed: - exp.bed:
type: file type: file
...@@ -8,7 +8,7 @@ peak_call: ...@@ -8,7 +8,7 @@ peak_call:
outputs: outputs:
- exp.tagAlign: - exp.tagAlign:
type: file type: file
- mv_bed_tagalign: - cp_bed_tagalign:
inputs: inputs:
- control.bed: - control.bed:
type: file type: file
......
mv_bed_tagalign: cp_bed_tagalign:
inputs: inputs:
- bed: - bed:
type: file type: file
...@@ -6,7 +6,7 @@ mv_bed_tagalign: ...@@ -6,7 +6,7 @@ mv_bed_tagalign:
outputs: outputs:
- bed: - bed:
type: file type: file
command: mv_bed_tagalign.sh command: cp
arguments: arguments:
- "$inputs.0": - "$inputs.0":
changeable: false changeable: false
......
File mode changed from 100644 to 100755
...@@ -2,4 +2,11 @@ ...@@ -2,4 +2,11 @@
. /util/opt/lmod/lmod/init/profile . /util/opt/lmod/lmod/init/profile
module load R spp module load R spp
Rscript ${SPP_NODUPS} "$@" newargs=()
while (( ${#@} ))
do
newargs+=("$1=$2")
shift
shift
done
Rscript ${SPP_NODUPS} "${newargs[@]/#/}"
...@@ -107,6 +107,13 @@ class Workflow(object): ...@@ -107,6 +107,13 @@ class Workflow(object):
if self.debug: if self.debug:
print "[LOAD_EXECUTABLE] %s" % (f,) print "[LOAD_EXECUTABLE] %s" % (f,)
break 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 # Overwrite pegasus::transfer to request more walltime
""" """
if self.config["profile"]["env"]["PEGASUS_HOME"]: if self.config["profile"]["env"]["PEGASUS_HOME"]:
......
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