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

@@ -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} \

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  );

spim_registration/timelapse/tomancak_test_cluster.yaml

 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",