Tested and debugged compress, resaving and splitting

But needs to be rewritten and merged onto a single Fiji

spim_registration/tools/compress/create-compress-jobs.sh

 #!/bin/bash
 
 # path of master file
-source ../../master_preprocessing.sh
+source ../master_preprocessing.sh
 
 # creates directory for job files if not present
 mkdir -p $jobs_compress
@@ -11,14 +11,14 @@ echo $czi_compress
 
 # splits up resaving into 1 job per .czi file and writes the given parameters
 # into the job file
-for i in $parallel_timepoints
+for i in $timepoints
 
 do
 	for a in $angle_prep
 	do
 		job="$jobs_compress/compress-$i-$a.job"
 		echo $job
-		echo "$XVFB_RUN -a $Fiji_resave \
+		echo "$XVFB_RUN $sysconfcpus $Fiji_resave \
 			-Ddir=$image_file_directory \
 			-Dtimepoint=$i \
 			-Dangle=$a \

spim_registration/tools/compress/submit-jobs

@@ -2,5 +2,5 @@
 
 for file in `ls ${1} | grep ".job$"`
 do
-	bsub -q short -n 4 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
+	bsub -q short -n 2 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
 done

spim_registration/tools/czi_resave/#checkpoint.sh#

-#!/bin/bash
-
-source ../../master_preprocessing.sh
-
-timepoint=`seq 0 391`
-dir=/projects/pilot_spim/Christopher/2014-10-23_H2A_gsb_G3/
-num_angles=1
-pad=3
-
-job_dir=/projects/pilot_spim/Christopher/pipeline_3.0/jobs_alpha_3.1/czi_resave/
-
-
-for i in $timepoint
-
-	do
-		i=`printf "%0${pad}d" "$i"`
-		num=$(ls $dir/spim_TL"$i"_Angle*.tif |wc -l)
-
-			if [ $num  -ne $num_angles ]
-
-	then
-		echo "TL"$i": TP or angles missing"
-		//bsub -q short -n 4 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/*${i}*
-
-	else
-		echo "TL"$i": Correct"
-
-fi
-
-done

spim_registration/tools/czi_resave/checkpoint.sh

-#!/bin/bash
-
-source ../../master_preprocessing.sh
-
-timepoint=`seq 0 391`
-dir=/projects/pilot_spim/Christopher/2014-10-23_H2A_gsb_G3/
-num_angles=1
-pad=3
-
-job_dir=/projects/pilot_spim/Christopher/pipeline_3.0/jobs_alpha_3.1/czi_resave/
-
-
-for i in $timepoint
-
-	do
-		i=`printf "%0${pad}d" "$i"`
-		num=$(ls $dir/spim_TL"$i"_Angle*.tif |wc -l)
-
-			if [ $num  -ne $num_angles ]
-
-	then
-		echo "TL"$i": TP or angles missing"
-		//bsub -q short -n 4 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/*${i}*
-
-	else
-		echo "TL"$i": Correct"
-
-fi
-
-done

spim_registration/tools/czi_resave/create-resaving-jobs.sh

 #!/bin/bash
 
 # path of master file
-source ../../master_preprocessing.sh
+source ../master_preprocessing.sh
 
 # creates directory for job files if not present
 mkdir -p $jobs_resaving
 
 # splits up resaving into 1 job per .czi file and writes the given parameters
 # into the job file
-for i in $parallel_timepoints
+for i in $timepoints
 
 do
 	for a in $angle_prep
 	do
 		job="$jobs_resaving/resave-$i-$a.job"
 		echo $job
-		echo "$XVFB_RUN -a $Fiji_resave \
+		echo "$XVFB_RUN $sysconfcpus $Fiji_resave \
 			-Ddir=$image_file_directory \
 			-Dtimepoint=$i \
 			-Dangle=$a \

spim_registration/tools/czi_resave/submit-jobs

@@ -2,5 +2,5 @@
 
 for file in `ls ${1} | grep ".job$"`
 do
-	bsub -q short -n 4 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
+	bsub -q short -n 2 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
 done

spim_registration/tools/master_preprocessing.sh

@@ -31,10 +31,10 @@ job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registr
 # Important: For renaming and resaving .czi files the first .czi file has to
 # carry the index (0)
 #-------------------------------------------------------------------------------
-
-pad="2"		# for padded zeros
+timepoints="`seq 0 1`" # number of time points format: "`seq 0 1`"
 angle_prep="1 2 3 4 5" # angles format: "1 2 3"
-
+pad="2"		# for padded zeros
+num_angles="5"
 #--- Renaming ------------------------------------------------------------------
 
 first_index="0"		# First index of czi files
@@ -48,8 +48,9 @@ target_pattern=spim_TL\{timepoint\}_Angle\{angle\}.czi	# The output pattern of r
 #-------------------------------------------------------------------------------
 # Fiji settings
 #-------------------------------------------------------------------------------
-XVFB_RUN="/sw/bin/xvfb-run" # virtual frame buffer
-
+XVFB_RUN="/sw/bin/xvfb-run -a" # virtual frame buffer
+sysconfcpus="sysconfcpus -n 2"
+Fiji: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64"
 Fiji_resave="/sw/users/schmied/packages/2014-06-02_Fiji.app_lifeline/ImageJ-linux64" # Fiji that works for resaving
 #-------------------------------------------------------------------------------
 # Pre-processing

spim_registration/tools/split_channels/create-split-jobs.sh

 #!/bin/bash
 
-source ../../master_preprocessing.sh
+source ../master_preprocessing.sh
 
 mkdir -p ${jobs_split}
 
@@ -13,7 +13,7 @@ for i in $parallel_timepoints
 				job="$jobs_split/split-$i-$a.job"
 				echo $job
 				echo "#!/bin/bash" > "$job"
-				echo "$XVFB_RUN -a $Fiji \
+				echo "$XVFB_RUN $sysconfcpus $Fiji \
 				-Dimage_file_directory=$image_file_directory \
 				-Dparallel_timepoints=$i \
 				-Dangle_prep=$a \