From f2ec1071406c4cbc4ea1243caadfe1de3d3fbc6c Mon Sep 17 00:00:00 2001
From: fabrice <fabrice.allain@pasteur.fr>
Date: Tue, 5 Apr 2016 11:06:21 +0200
Subject: [PATCH] Removed working directory path in .ini file. ariaproject now
generated using outdir command line arg
---
ariaec/__init__.pyc | Bin 235 -> 235 bytes
ariaec/base.pyc | Bin 10170 -> 10170 bytes
ariaec/commands.pyc | Bin 10416 -> 10416 bytes
ariaec/conf/aria_ec.ini | 1 -
ariaec/econverter.py | 29 ++++++++++++++++++-----------
ariaec/econverter.pyc | Bin 27497 -> 27715 bytes
ariaec/ecsettings.pyc | Bin 7215 -> 7215 bytes
ariaec/maplot.pyc | Bin 5130 -> 5130 bytes
ariaec/protein.pyc | Bin 15924 -> 15924 bytes
ariaec/protmap.pyc | Bin 45056 -> 45056 bytes
ariaec/reader.pyc | Bin 19170 -> 19170 bytes
ariaec/setup.pyc | Bin 7818 -> 7818 bytes
version.py | 2 +-
13 files changed, 19 insertions(+), 13 deletions(-)
diff --git a/ariaec/__init__.pyc b/ariaec/__init__.pyc
index 42b779115f1d982b021de34a3c088eee58d048d0..8beec7da806c597f90cc1923e67032e7aa62f134 100644
GIT binary patch
delta 14
VcmaFO_?nT8`7<xq8?lLOPXQ<*1!@2Q
delta 14
VcmaFO_?nT8`7<xqAC-x0PXQ>Z1&9Cu
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index f4a63e0bc26248ccb20121c00f6978ce683ea0ab..d6f1402e1fc0c50fce3f807e87cb99c13241e5d5 100644
GIT binary patch
delta 15
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delta 15
WcmdnxzssME`7<xqD*cUYThswBQU#F!
diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index 0986351f81727604baf3a0aa6c042b6851c464f2..e58e41ac9f3a8f238b0b9abc9e6e13b9066d6d5a 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/ariaec/conf/aria_ec.ini b/ariaec/conf/aria_ec.ini
index d47d9cf..a36fcfa 100644
--- a/ariaec/conf/aria_ec.ini
+++ b/ariaec/conf/aria_ec.ini
@@ -73,7 +73,6 @@ nd_control: 0
runid: 1
cpus: 100
host_command: sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
-working_directory: data/examples/out/setup
temp_root: data/examples/out/setup
parameter_definition: automatic
ss_dist_format: tbl
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index ea62118..e9b7668 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -712,6 +712,15 @@ class AriaEcXMLConverter(AriaXMLConverter):
def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files,
desc=""):
+ """
+ Generate ariaproject.xml file
+ :param aria_template: ariaproject.xml template path
+ :param seqfile:
+ :param dist_files:
+ :param tbl_files:
+ :param desc:
+ :return:
+ """
if aria_template:
template = os.path.abspath(aria_template)
@@ -737,26 +746,24 @@ class AriaEcXMLConverter(AriaXMLConverter):
'the ratio %.2f:%.2f' % (steps_1, steps_2))
aria_project_dict.update(self.settings.setup.config)
- work_dir = os.path.abspath(aria_project_dict['working_directory'])
+ work_dir = os.path.abspath(self.settings.outdir)
temp_root = os.path.abspath(aria_project_dict['temp_root'])
if not os.path.exists(work_dir) or not os.path.exists(temp_root):
- logger.info("Working dir %s and temp directory %s doesn't exist." % (
- work_dir, temp_root))
+ logger.info("Working dir %s doesn't exist." % work_dir)
logger.info("Create new directory %s" % work_dir)
os.makedirs(work_dir)
+
+ if not os.path.exists(temp_root):
+ logger.info("Temp directory %s doesn't exist." % temp_root)
logger.info("Create new directory %s" % temp_root)
os.makedirs(temp_root)
- for direct in (work_dir, temp_root):
-
- if not os.path.exists(os.path.join(direct, self.outprefix)):
- os.makedirs(os.path.join(direct, self.outprefix))
-
- if not os.path.exists(os.path.join(direct, self.outprefix, desc)):
- os.makedirs(os.path.join(direct, self.outprefix, desc))
+ if not os.path.exists(os.path.join(temp_root, self.outprefix)):
+ os.makedirs(os.path.join(temp_root, self.outprefix))
+ if not os.path.exists(os.path.join(temp_root, self.outprefix, desc)):
+ os.makedirs(os.path.join(temp_root, self.outprefix, desc))
- work_dir = os.path.join(work_dir, self.outprefix, desc)
temp_root = os.path.join(temp_root, self.outprefix, desc)
aria_project_dict['working_directory'] = work_dir
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 1e89d37d3a6835f86c91c4bcacca99b2cd3c8bbe..b86dacd13ed269c6f95c4e984d70cd0ade0610d3 100644
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diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 209f3ab6b90d317fbeb8c04d9881955e3da2623d..14a6ab0431a6f0549d2010cb1be33f34717c8df2 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index a21fef1bed62dd942c979bb3f41cec9c39e17d56..f774d93fd4dbee644841d77ba4619ebb527daa0e 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 284b67088a7c769f0534a12991a39d4cbd2b4cf9..9384a753ca62347a0205225fbddc43a197d46c95 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
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diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index fada925ea836ec7c758856a3e4ef48a20448ebc7..32c3329cf97c194f6d91309a7ffd312a215a9608 100644
GIT binary patch
delta 17
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diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index 4f16a2b361a1c02638a25850235bf1943cb5f8fb..9acd618838fbdac5ab9e9b455d1417883426c65d 100644
GIT binary patch
delta 15
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delta 15
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diff --git a/version.py b/version.py
index 70bb331..282deff 100644
--- a/version.py
+++ b/version.py
@@ -1,2 +1,2 @@
# Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev1
\ No newline at end of file
+__version__=v0.1.11-dev2
\ No newline at end of file
--
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