From 8208fb6c0e011859f09dd7541ce68ef2a3b4ad6a Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Sun, 5 Jul 2015 17:44:37 +0200
Subject: [PATCH] Cleaned up config file, debugged and tested it
---
spim_registration/timelapse/Snakefile | 16 +++++++---------
spim_registration/timelapse/single_test.yaml | 3 ---
2 files changed, 7 insertions(+), 12 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index f7211ce..c6dab52 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -7,9 +7,9 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
JOBDIR+="/"
# Test config file single Channel:
-# configfile: "single_test.yaml"
+configfile: "single_test.yaml"
# Test config file dual channel one channel contains beads:
-configfile: "dual_OneChannel.yaml"
+# configfile: "dual_OneChannel.yaml"
# data specific config file, expected to be inside JOBDIR
# configfile: "tomancak_test_cluster.yaml"
@@ -32,7 +32,7 @@ rule resave_prepared:
# defining xml for czi dataset
rule define_xml_czi:
- input:glob.glob('*.czi'), config["define_xml_czi"]["first_czi"]
+ input:glob.glob('*.czi'), config["common"]["first_czi"]
output: config["common"]["first_xml_filename"] + ".xml"
log: "define_xml_czi.log"
run:
@@ -60,7 +60,7 @@ rule define_xml_czi:
# defining xml for tif dataset
rule define_xml_tif:
- input: glob.glob(re.sub("{{.}}","*",config["define_xml_tif"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
+ input: glob.glob(re.sub("{{.}}","*",config["common"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
output: config["common"]["first_xml_filename"] + ".xml"
log: "define_xml_tif.log"
run:
@@ -119,7 +119,6 @@ rule hdf5_xml:
-Drun_only_job_number=0 \
-- --no-splash {path_bsh}""",
config["common"],
- config["define_xml_czi"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
@@ -150,7 +149,6 @@ rule resave_hdf5:
-Drun_only_job_number={job_number} \
-- --no-splash {path_bsh}""", # the & submits everyting at once
config["common"],
- config["define_xml_czi"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
@@ -411,7 +409,7 @@ rule deconvolution:
rule define_output:
input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
- output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
+ output: config["common"]["output_xml"].strip('\"') + ".xml"
log: "define_output.log"
run:
cmd_string = produce_string(
@@ -442,7 +440,7 @@ rule define_output:
# create mother .xml/.h5
rule hdf5_xml_output:
- input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
+ input: config["common"]["output_xml"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
[ item+"_output" for item in datasets ]
log: "output_hdf5_xml.log"
@@ -470,7 +468,7 @@ rule hdf5_xml_output:
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_hdf5"])
- part_string += " > {log} 2>&1 && touch {output}"
+ part_string += " > {log} 2>&1"
shell(part_string)
rule resave_hdf5_output:
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
index 10b770e..3171fb1 100755
--- a/spim_registration/timelapse/single_test.yaml
+++ b/spim_registration/timelapse/single_test.yaml
@@ -179,9 +179,6 @@ common: {
# File type
output_data_type: "16Bit" # "32Bit" or "16Bit"
}
- # ============================================================================
- # Advanced Settings
- # ============================================================================
define_xml_czi: {
rotation_around: "X-Axis", # axis of acquistion
--
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