diff --git a/spim_registration/tools/compress/create-compress-jobs.sh b/spim_registration/tools/compress/create-compress-jobs.sh
index 2f5009a713f19d503da43e276bcced3cc8197648..e4e869b39b0546f9c128d3791f33c10bd7137c09 100755
--- a/spim_registration/tools/compress/create-compress-jobs.sh
+++ b/spim_registration/tools/compress/create-compress-jobs.sh
@@ -1,7 +1,7 @@
#!/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 \
diff --git a/spim_registration/tools/compress/submit-jobs b/spim_registration/tools/compress/submit-jobs
index 945496d595d8700e1d3976be2deba06c0947e800..626449c2bfc64732d0467b6f20cff8cb6060d2a7 100755
--- a/spim_registration/tools/compress/submit-jobs
+++ b/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
diff --git a/spim_registration/tools/czi_resave/#checkpoint.sh# b/spim_registration/tools/czi_resave/#checkpoint.sh#
deleted file mode 100755
index 7442db5909ada1ddf48c8ce377c2b2bfe4ce69bb..0000000000000000000000000000000000000000
--- a/spim_registration/tools/czi_resave/#checkpoint.sh#
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/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
diff --git a/spim_registration/tools/czi_resave/checkpoint.sh b/spim_registration/tools/czi_resave/checkpoint.sh
deleted file mode 100755
index 7442db5909ada1ddf48c8ce377c2b2bfe4ce69bb..0000000000000000000000000000000000000000
--- a/spim_registration/tools/czi_resave/checkpoint.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/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
diff --git a/spim_registration/tools/czi_resave/create-resaving-jobs.sh b/spim_registration/tools/czi_resave/create-resaving-jobs.sh
index 5c21db6049b1a22e1102db1a4bc36b05f1ae8dcf..200bc1a50935f74af511382c9c7aba46d9f1fa20 100755
--- a/spim_registration/tools/czi_resave/create-resaving-jobs.sh
+++ b/spim_registration/tools/czi_resave/create-resaving-jobs.sh
@@ -1,21 +1,21 @@
#!/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 \
diff --git a/spim_registration/tools/czi_resave/submit-jobs b/spim_registration/tools/czi_resave/submit-jobs
index 945496d595d8700e1d3976be2deba06c0947e800..626449c2bfc64732d0467b6f20cff8cb6060d2a7 100755
--- a/spim_registration/tools/czi_resave/submit-jobs
+++ b/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
diff --git a/spim_registration/tools/master_preprocessing.sh b/spim_registration/tools/master_preprocessing.sh
index b0a2ca6ed45f1b5897472de3c32b6643fe9e39ab..74a9ba09898ba51ed24de4a04f5aafba420629d9 100755
--- a/spim_registration/tools/master_preprocessing.sh
+++ b/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
diff --git a/spim_registration/tools/split_channels/create-split-jobs.sh b/spim_registration/tools/split_channels/create-split-jobs.sh
index 2a1b873a3587ff33dc6c964a6c333d0674b871c8..1491121f8a77251244c68d2fb5016a269e9ec1db 100755
--- a/spim_registration/tools/split_channels/create-split-jobs.sh
+++ b/spim_registration/tools/split_channels/create-split-jobs.sh
@@ -1,6 +1,6 @@
#!/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 \