From 7c52fdd99f6993bf1d4323fc3f13b01a4493dec3 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Mon, 15 Jun 2015 14:28:54 +0200
Subject: [PATCH] Fixed bugs in deconvolution.bsh
compute_on is not present in Snakefile
compute_on, directory_cuda and cudafourierconvolution System.getProperty
now correct
---
spim_registration/timelapse/Snakefile | 1 +
spim_registration/timelapse/deconvolution.bsh | 6 +++---
spim_registration/timelapse/tomancak_test_cluster.yaml | 2 +-
3 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index d0c6c72..46f603e 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -386,6 +386,7 @@ rule deconvolution:
-Dosem_acceleration={osem_acceleration} \
-DTikhonov_parameter={Tikhonov_parameter} \
-Dcompute={compute} \
+ -Dcompute_on={compute_on} \
-Dcudafourierconvolution={cudafourierconvolution} \
-Dpsf_estimation={psf_estimation} \
-Ddirectory_cuda={directory_cuda} \
diff --git a/spim_registration/timelapse/deconvolution.bsh b/spim_registration/timelapse/deconvolution.bsh
index 6bf9b49..1ecd9b9 100755
--- a/spim_registration/timelapse/deconvolution.bsh
+++ b/spim_registration/timelapse/deconvolution.bsh
@@ -122,9 +122,9 @@ System.out.println( channel_string );
System.out.println( "-------------------------------------------------------" );
System.out.println( "GPU/CPU setting: " );
-compute_on = System.getProperty( "compute_on = " + compute_on );
-directory_cuda = System.getProperty( "directory_cuda = " + directory_cuda );
-System.getProperty( "cudafourierconvolution = " + cudafourierconvolution );
+compute_on = System.getProperty( "compute_on" );
+directory_cuda = System.getProperty( "directory_cuda" );
+cudafourierconvolution = System.getProperty( "cudafourierconvolution" );
System.out.println( "compute_on = " + compute_on );
System.out.println( "directory_cuda = " + directory_cuda );
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 4819870..3bd147a 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -1,7 +1,7 @@
common: {
# directory that contains the bean shell scripts
bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- directory_cuda: "/sw/users/schmied/packages/cuda/lib/",
+ directory_cuda: "/sw/users/schmied/cuda/",
#fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
fiji-prefix: "/sw/bin/xvfb-run -a",
--
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