From 6f3e8c958f95f81b0b4009bbf4181cc4eda25701 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Tue, 7 Jul 2015 22:08:39 +0200
Subject: [PATCH] Testing temp files
---
spim_registration/timelapse/Snakefile | 24 ++++++++++++------------
spim_registration/timelapse/fusion.bsh | 2 +-
2 files changed, 13 insertions(+), 13 deletions(-)
mode change 100644 => 100755 spim_registration/timelapse/Snakefile
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
old mode 100644
new mode 100755
index 50f2e0a..20eccb8
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -105,7 +105,7 @@ ruleorder: define_xml_czi > define_xml_tif
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 ]
+ temp([ item+"_xml" for item in datasets ])
log: "logs/b1_hdf5_xml.log"
run:
part_string = produce_string(
@@ -135,7 +135,7 @@ rule hdf5_xml:
# resave .czi/.tif dataset as hdf5
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"
+ output: "{xml_base}-{file_id,\d+}-00.h5", temp("{xml_base}-{file_id,\d+}-00.h5_hdf5")
log: "logs/b2_resave_hdf5-{file_id}.log"
run:
part_string = produce_string(
@@ -164,7 +164,7 @@ 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",
+ output: temp("{xml_base}.job_{file_id,\d+}.xml")#, "{xml_base}-{file_id,\d+}-00.h5_registered",
log: "logs/c_{xml_base}-{file_id}-registration.log"
run:
cmd_string = produce_string(
@@ -236,7 +236,7 @@ rule xml_merge:
rule timelapse:
input: rules.xml_merge.output
- output: rules.xml_merge.output[0] + "_timelapse"
+ output: temp(rules.xml_merge.output[0] + "_timelapse")
log: "logs/d2_{xml_base}_timelapse.log"
run:
cmd_string = produce_string(
@@ -296,7 +296,7 @@ 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"
+ output: temp("{xml_base}-{file_id,\d+}-00.h5_fusion")
log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
@@ -367,7 +367,7 @@ 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"
+ output: temp("{xml_base}-{file_id,\d+}-00.h5_deconvolution")
log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string(
@@ -414,7 +414,7 @@ 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"
+ output: temp(config["common"]["output_xml"].strip('\"') + ".xml")
log: "logs/f1_define_output.log"
run:
cmd_string = produce_string(
@@ -447,7 +447,7 @@ rule define_output:
rule hdf5_xml_output:
input: config["common"]["output_xml"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
- [ item+"_output" for item in datasets ]
+ temp([ item+"_output" for item in datasets ])
log: "logs/f2_output_hdf5_xml.log"
run:
part_string = produce_string(
@@ -478,7 +478,7 @@ rule hdf5_xml_output:
rule resave_hdf5_output:
input: rules.hdf5_xml_output.output
- output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
+ output: temp("{xml_base}-{file_id,\d+}-00.h5_output_hdf5")
log: "logs/f3_resave_output-{file_id}.log"
run:
part_string = produce_string(
@@ -518,7 +518,7 @@ rule distclean:
# NOTE! The following enables mailing, which will send out a mail once an entire workflow is done (the below does not include anything in the message body, redirect from /dev/null)
# onsuccess:
-# shell("mail -s \"[SUCCESS] our_cluster:{jdir} finished \" xxx@mpi-cbg.de < /dev/null".format(jdir=JOBDIR))
+# shell("mail -s \"[SUCCESS] our_cluster:{jdir} finished \" schmied@mpi-cbg.de < /dev/null".format(jdir=JOBDIR))
-# onerror:
-# shell("mail -s \"[ERROR] out_cluster:{jdir}\" xxx@mpi-cbg.de < /dev/null".format(jdir=JOBDIR))
+onerror:
+ shell("mail -s \"[ERROR] out_cluster:{jdir}\" schmied@mpi-cbg.de < /dev/null".format(jdir=JOBDIR))
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
index 945556c..cdc86a0 100644
--- a/spim_registration/timelapse/fusion.bsh
+++ b/spim_registration/timelapse/fusion.bsh
@@ -99,7 +99,7 @@ IJ.run("Fuse/Deconvolve Dataset",
"process_views_in_paralell=All " +
"interpolation=[" + interpolation + "] " +
"blend " +
- "content-based " +
+ //"content-based " +
"output_file_directory=" + image_file_directory + " " +
"lossless " +
"imglib2_data_container=[" + imglib2_data_container + "]");
--
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