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Metagenomics
snakemake
Commits
ba3a4101
Commit
ba3a4101
authored
May 16, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
add module dependency for graphlan
parent
f2052487
Changes
3
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Inline
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tools/graphlan/export2graphlan/Snakefile
View file @
ba3a4101
__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
tools/graphlan/graphlan/Snakefile
View file @
ba3a4101
__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
tools/graphlan/graphlan_annotate/Snakefile
View file @
ba3a4101
__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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