From 004093f58cb0bc478f57e7ca7949e77bac17e484 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Sun, 5 Jul 2015 19:06:36 +0200
Subject: [PATCH] Log files are written into log directory in data directory
Log files are ordered
---
spim_registration/timelapse/Snakefile | 28 +++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 6c6b744..4aa60fa 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -34,7 +34,7 @@ rule resave_prepared:
rule define_xml_czi:
input:glob.glob('*.czi'), config["common"]["first_czi"]
output: config["common"]["first_xml_filename"] + ".xml"
- log: "define_xml_czi.log"
+ log: "logs/a1_define_xml_czi.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
@@ -62,7 +62,7 @@ rule define_xml_czi:
rule define_xml_tif:
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"
+ log: "logs/a2_define_xml_tif.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -101,7 +101,7 @@ rule hdf5_xml:
input: config["common"]["first_xml_filename"] + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
[ item+"_xml" for item in datasets ]
- log: "hdf5_xml.log"
+ log: "logs/b1_hdf5_xml.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -131,7 +131,7 @@ rule hdf5_xml:
rule resave_hdf5:
input: rules.hdf5_xml.output # "{xml_base}-{file_id,\d+}-00.h5_xml"
output: "{xml_base}-{file_id,\d+}-00.h5", "{xml_base}-{file_id,\d+}-00.h5_hdf5"
- log: "resave_hdf5-{file_id}.log"
+ log: "logs/b2_resave_hdf5-{file_id}.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -160,7 +160,7 @@ rule resave_hdf5:
rule registration:
input: "{xml_base}-{file_id}-00.h5"
output: "{xml_base}.job_{file_id,\d+}.xml"#, "{xml_base}-{file_id,\d+}-00.h5_registered",
- log: "{xml_base}-{file_id}-registration.log"
+ log: "logs/c_{xml_base}-{file_id}-registration.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -214,7 +214,7 @@ rule registration:
rule xml_merge:
input: [ str(config["common"]["hdf5_xml_filename"].strip('\"')+".job_"+(padding_format.format(item))+".xml") for item in range(int(config["common"]["ntimepoints"])) ] #[ item+"_registered" for item in datasets ]
output: "{xml_base}_merge.xml"
- log: "{xml_base}_merge.log"
+ log: "logs/d1_{xml_base}_merge.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -232,7 +232,7 @@ rule xml_merge:
rule timelapse:
input: rules.xml_merge.output
output: rules.xml_merge.output[0] + "_timelapse"
- log: "{xml_base}_timelapse.log"
+ log: "logs/d2_{xml_base}_timelapse.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -265,7 +265,7 @@ rule timelapse:
rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
output: rules.timelapse.output[0] + "_duplicate"
- log: "{xml_base}_duplicate_transformations.log"
+ log: "logs/d3_{xml_base}_duplicate_transformations.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -292,7 +292,7 @@ rule duplicate_transformations:
rule fusion:
input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
- log: "{xml_base}-{file_id,\d+}-00-fusion.log"
+ log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -335,7 +335,7 @@ rule fusion:
rule external_transform:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
output: rules.timelapse.output[0] + "_external_trafo"
- log: "external_transform.log"
+ log: "logs/e2_external_transform.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -363,7 +363,7 @@ rule external_transform:
rule deconvolution:
input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
- log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
+ log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -410,7 +410,7 @@ rule deconvolution:
rule define_output:
input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
output: config["common"]["output_xml"].strip('\"') + ".xml"
- log: "define_output.log"
+ log: "logs/f1_define_output.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -443,7 +443,7 @@ rule hdf5_xml_output:
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"
+ log: "logs/f2_output_hdf5_xml.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -474,7 +474,7 @@ rule hdf5_xml_output:
rule resave_hdf5_output:
input: rules.hdf5_xml_output.output
output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
- log: "resave_output-{file_id}.log"
+ log: "logs/f3_resave_output-{file_id}.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
--
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