From ba3a4101ec47879755872623d083b4d374d43ba2 Mon Sep 17 00:00:00 2001
From: kehillio <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 16 May 2019 17:12:00 +0200
Subject: [PATCH] add module dependency for graphlan
---
tools/graphlan/export2graphlan/Snakefile | 14 ++++++++++----
tools/graphlan/graphlan/Snakefile | 14 ++++++++++----
tools/graphlan/graphlan_annotate/Snakefile | 14 ++++++++++----
3 files changed, 30 insertions(+), 12 deletions(-)
diff --git a/tools/graphlan/export2graphlan/Snakefile b/tools/graphlan/export2graphlan/Snakefile
index 448fcf0..05b030c 100644
--- a/tools/graphlan/export2graphlan/Snakefile
+++ b/tools/graphlan/export2graphlan/Snakefile
@@ -1,5 +1,6 @@
-__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
diff --git a/tools/graphlan/graphlan/Snakefile b/tools/graphlan/graphlan/Snakefile
index 62f7a23..6617e1b 100644
--- a/tools/graphlan/graphlan/Snakefile
+++ b/tools/graphlan/graphlan/Snakefile
@@ -1,5 +1,6 @@
-__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
diff --git a/tools/graphlan/graphlan_annotate/Snakefile b/tools/graphlan/graphlan_annotate/Snakefile
index 6a1b117..3a26ca9 100644
--- a/tools/graphlan/graphlan_annotate/Snakefile
+++ b/tools/graphlan/graphlan_annotate/Snakefile
@@ -1,5 +1,6 @@
-__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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