Commit ba3a4101 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add module dependency for graphlan

parent f2052487
__export2graphlan_exec_command = config['export2graphlan'].get('exec_command', 'export2graphlan.py')
__export2graphlan_options = config['export2graphlan'].get('options', "")
__export2graphlan_exec_command = config.get('export2graphlan', {}).get('exec_command', 'export2graphlan.py')
__export2graphlan_modules = config.get('export2graphlan', {}).get('modules')
__export2graphlan_options = config.get('export2graphlan', {}).get('options', "")
rule export2graphlan:
input:
......@@ -9,6 +10,11 @@ rule export2graphlan:
annot = __export2graphlan_output_annotation
params:
exec_command = __export2graphlan_exec_command,
modules = __export2graphlan_modules,
options = __export2graphlan_options
shell:
"{params.exec_command} {params.options} -i {input} --tree {output.tree} --annotation {output.annot}"
run:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} {params.options} -i {input} --tree {output.tree} --annotation {output.annot}")
shell(" && ".join(command))
\ No newline at end of file
__graphlan_exec_command = config['graphlan'].get('exec_command', 'graphlan.py')
__graphlan_options = config['graphlan'].get('options', "")
__graphlan_exec_command = config.get('graphlan', {}).get('exec_command', 'graphlan.py')
__graphlan_modules = config.get('graphlan', {}).get('modules')
__graphlan_options = config.get('graphlan', {}).get('options', "")
rule graphlan:
input:
......@@ -8,6 +9,11 @@ rule graphlan:
__graphlan_output
params:
exec_command = __graphlan_exec_command,
modules = __graphlan_modules,
options = __graphlan_options
shell:
"{params.exec_command} {params.options} {input} {output}"
run:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} {params.options} {input} {output}")
shell(" && ".join(command))
\ No newline at end of file
__graphlan_annotate_exec_command = config['graphlan_annotate'].get('exec_command', 'graphlan_annotate.py')
__graphlan_annotate_options = config['graphlan_annotate'].get('options', "")
__graphlan_annotate_exec_command = config.get('graphlan_annotate', {}).get('exec_command', 'graphlan_annotate.py')
__graphlan_annotate_modules = config.get('graphlan_annotate', {}).get('modules')
__graphlan_annotate_options = config.get('graphlan_annotate', {}).get('options', "")
rule graphlan_annotate:
input:
......@@ -9,6 +10,11 @@ rule graphlan_annotate:
__graphlan_annotate_output
params:
exec_command = __graphlan_annotate_exec_command,
modules = __graphlan_annotate_modules,
options = __graphlan_annotate_options
shell:
"{params.exec_command} {params.options} --annot {input.annot} {input.tree} {output}"
run:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} {params.options} --annot {input.annot} {input.tree} {output}")
shell(" && ".join(command))
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