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chyuminchyumin
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compiled_name backcompatible, minor improvements
1 parent e982e0a commit 439b1df

13 files changed

Lines changed: 52 additions & 44 deletions

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‎hdsort-compiled/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
FROM hdsort-matlab-base
22

3-
RUN chmod 755 /usr/bin/mlrtapp/hdsort_master
3+
RUN chmod 755 /usr/bin/mlrtapp/hdsort_compiled
44
ENV PATH="/usr/bin/mlrtapp:${PATH}"
55

66
# Installing Python with miniconda

‎hdsort-compiled/compile.sh‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -13,26 +13,26 @@ if [ $# -ne 2 ]; then
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exit 1
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fi
1515

16-
WC_PATH=$1
17-
SI_PATH=$2
16+
HDSORT_COMPILED_NAME="hdsort_compiled"
17+
HDSORT_PATH=${1%/}
18+
SI_PATH=${2%/}
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WORK_DIR=$(pwd)
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SOURCE_DIR=$( dirname -- "$0"; )
2021
TMP_DIR=$SOURCE_DIR/tmp
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22-
echo "hdsort path: ${WC_PATH}"
23+
echo "hdsort path: ${HDSORT_PATH}"
2324
echo "spike-interface path: ${SI_PATH}"
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2526
echo "Creating tmp folder: $TMP_DIR"
2627
cd $WORK_DIR
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mkdir -p $TMP_DIR
2829

29-
echo "Compiling hdsort_master..."
30+
echo "Compiling hdsort..."
3031
cd $TMP_DIR
31-
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/hdsort/hdsort_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${WC_PATH}"
32+
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/hdsort/hdsort_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${HDSORT_PATH} -o ${HDSORT_COMPILED_NAME}"
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3334
echo "Creating base docker image..."
34-
matlab -batch "compiler.package.docker('hdsort_master', 'requiredMCRProducts.txt', 'ImageName', 'hdsort-matlab-base')"
35+
matlab -batch "compiler.package.docker('${HDSORT_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'hdsort-matlab-base')"
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cd $WORK_DIR
3738
rm -r $TMP_DIR
38-

‎ironclust-compiled/compile.sh‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,8 @@ if [ $# -ne 1 ]; then
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exit 1
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fi
1313

14-
IC_PATH=$1/matlab
15-
14+
IC_COMPILED_NAME="p_ironclust"
15+
IC_PATH=${1%/}/matlab
1616
WORK_DIR=$(pwd)
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SOURCE_DIR=$( dirname -- "$0"; )
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TMP_DIR=$SOURCE_DIR/tmp
@@ -32,18 +32,18 @@ cd $TMP_DIR
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3333
# Generating multiple "-a filename" string
3434
# This is needed because wildcard pattern /* doesn't work
35-
# properly when running outside matlab's console
35+
# properly when running mcc outside matlab's console
3636
ADD_FILES=""
3737
for fname in $(eval "ls ${IC_PATH} -I \"*.pdf\" -p | grep -v /"); do
3838
ADD_FILES="${ADD_FILES} -a ${IC_PATH}/${fname}"
3939
done
4040
ADD_FILES="${ADD_FILES} -a ${IC_PATH}/prb"
4141
ADD_FILES="${ADD_FILES} -a ${IC_PATH}/prb_json"
4242

43-
matlab -batch "mcc -m ${IC_PATH}/p_ironclust.m ${ADD_FILES}"
43+
matlab -batch "mcc -m ${IC_PATH}/p_ironclust.m ${ADD_FILES} -o ${IC_COMPILED_NAME}"
4444

4545
echo "Creating base docker image..."
46-
matlab -batch "compiler.package.docker('p_ironclust', 'requiredMCRProducts.txt', 'ImageName', 'ironclust-matlab-base')"
46+
matlab -batch "compiler.package.docker('${IC_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ironclust-matlab-base')"
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4848
cd $WORK_DIR
4949
rm -r $TMP_DIR

‎kilosort_no_license/kilosort-compiled/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
FROM ks-matlab-base
22

3-
RUN chmod 755 /usr/bin/mlrtapp/kilosort_master
3+
RUN chmod 755 /usr/bin/mlrtapp/ks_compiled
44
ENV PATH="/usr/bin/mlrtapp:${PATH}"
55

66
# Installing Python with miniconda

‎kilosort_no_license/kilosort-compiled/compile.sh‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,9 @@ if [ $# -ne 2 ]; then
1313
exit 1
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fi
1515

16-
KS_PATH=$1
17-
SI_PATH=$2
16+
KS_COMPILED_NAME="ks_compiled"
17+
KS_PATH=${1%/}
18+
SI_PATH=${2%/}
1819
WORK_DIR=$(pwd)
1920
SOURCE_DIR=$( dirname -- "$0"; )
2021
TMP_DIR=$SOURCE_DIR/tmp
@@ -32,10 +33,10 @@ mkdir -p $TMP_DIR
3233

3334
echo "Compiling kilosort_master..."
3435
cd $TMP_DIR
35-
matlab -batch "mcc -m $SI_PATH/spikeinterface/sorters/kilosort/kilosort_master.m -a $SI_PATH/spikeinterface/sorters/utils -a $KS_PATH"
36+
matlab -batch "mcc -m $SI_PATH/spikeinterface/sorters/kilosort/kilosort_master.m -a $SI_PATH/spikeinterface/sorters/utils -a $KS_PATH -o ${KS_COMPILED_NAME}"
3637

3738
echo "Creating base docker image..."
38-
matlab -batch "compiler.package.docker('kilosort_master', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')"
39+
matlab -batch "compiler.package.docker('${KS_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')"
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4041
cd $WORK_DIR
4142
rm -r $TMP_DIR

‎kilosort_no_license/kilosort2-compiled/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
FROM ks2-matlab-base
22

3-
RUN chmod 755 /usr/bin/mlrtapp/kilosort2_master
3+
RUN chmod 755 /usr/bin/mlrtapp/ks2_compiled
44
ENV PATH="/usr/bin/mlrtapp:${PATH}"
55

66
# Installing Python with miniconda

‎kilosort_no_license/kilosort2-compiled/compile.sh‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,9 @@ if [ $# -ne 2 ]; then
1313
exit 1
1414
fi
1515

16-
KS_PATH=$1
17-
SI_PATH=$2
16+
KS2_COMPILED_NAME="ks2_compiled"
17+
KS_PATH=${1%/}
18+
SI_PATH=${2%/}
1819
WORK_DIR=$(pwd)
1920
SOURCE_DIR=$( dirname -- "$0"; )
2021
TMP_DIR=$SOURCE_DIR/tmp
@@ -32,10 +33,10 @@ mkdir -p $TMP_DIR
3233

3334
echo "Compiling kilosort_master..."
3435
cd $TMP_DIR
35-
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
36+
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_COMPILED_NAME}"
3637

3738
echo "Creating base docker image..."
38-
matlab -batch "compiler.package.docker('kilosort2_master', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')"
39+
matlab -batch "compiler.package.docker('${KS2_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')"
3940

4041
cd $WORK_DIR
4142
rm -r $TMP_DIR

‎kilosort_no_license/kilosort2_5-compiled/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
FROM ks2_5-matlab-base
22

3-
RUN chmod 755 /usr/bin/mlrtapp/kilosort2_5_master
3+
RUN chmod 755 /usr/bin/mlrtapp/ks2_5_compiled
44
ENV PATH="/usr/bin/mlrtapp:${PATH}"
55

66
# Installing Python with miniconda

‎kilosort_no_license/kilosort2_5-compiled/compile.sh‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,9 @@ if [ $# -ne 2 ]; then
1313
exit 1
1414
fi
1515

16-
KS_PATH=$1
17-
SI_PATH=$2
16+
KS2_5_COMPILED_NAME="ks2_5_compiled"
17+
KS_PATH=${1%/}
18+
SI_PATH=${2%/}
1819
WORK_DIR=$(pwd)
1920
SOURCE_DIR=$( dirname -- "$0"; )
2021
TMP_DIR=$SOURCE_DIR/tmp
@@ -32,10 +33,10 @@ mkdir -p $TMP_DIR
3233

3334
echo "Compiling kilosort_master..."
3435
cd $TMP_DIR
35-
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2_5/kilosort2_5_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
36+
matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2_5/kilosort2_5_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_5_COMPILED_NAME}"
3637

3738
echo "Creating base docker image..."
38-
matlab -batch "compiler.package.docker('kilosort2_5_master', 'requiredMCRProducts.txt', 'ImageName', 'ks2_5-matlab-base')"
39+
matlab -batch "compiler.package.docker('${KS2_5_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks2_5-matlab-base')"
3940

4041
cd $WORK_DIR
4142
rm -r $TMP_DIR

‎kilosort_no_license/kilosort3-compiled/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
FROM ks3-matlab-base
22

3-
RUN chmod 755 /usr/bin/mlrtapp/kilosort3_master
3+
RUN chmod 755 /usr/bin/mlrtapp/ks3_compiled
44
ENV PATH="/usr/bin/mlrtapp:${PATH}"
55

66
# Installing Python with miniconda

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