remove debug code and updated Dockerfile

Author: lhhunghimself

.gitignore

@@ -14,3 +14,5 @@ log*
 features/
 msk*
 sc_test*
+.specstory
+

Dockerfile

@@ -1,22 +1,29 @@
-FROM debian:bookworm-slim as builder
+FROM debian:bookworm-slim AS builder
+ARG VERSION=1.0.0
 ARG DEBIAN_FRONTEND=noninteractive
-RUN apt-get -y update && apt-get -y install  build-essential zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgomp1 libglib2.0-dev libcairo2-dev
-ADD assignBarcodes.c /code/assignBarcodes.c
-ADD Makefile /code/Makefile
-ADD queue.h /code/queue.h
-ADD queue.c /code/queue.c
-ADD defines.h /code/defines.h
-ADD plasma*.h  /code/.
-WORKDIR /code
+RUN apt-get -y update && apt-get -y install  build-essential zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgomp1 libglib2.0-dev curl libcairo2-dev libx11-dev libxext-dev libxrender-dev
+RUN curl -L https://github.com/morphic-bio/process_features/archive/refs/tags/v${VERSION}.tar.gz | tar -xz
+WORKDIR /process_features-${VERSION}
 RUN make && mv assignBarcodes /usr/local/bin/assignBarcodes
-RUN apt-get -y remove build-essential && apt-get -y autoremove
 
 FROM debian:bookworm-slim
 COPY --from=builder /usr/local/bin/assignBarcodes /usr/local/bin/assignBarcodes
 #copy the zlib1g library and libglib2.0 libgomp.so.0
-COPY --from=builder /usr/lib/x86_64-linux-gnu/* /usr/lib/x86_64-linux-gnu/.
-# **Copy the font configuration files**
-COPY --from=builder /etc/fonts /etc/fonts
+#copy the libcairo2 libpixman-1 libfontconfig1 libfreetype6 libpng16 libxcb* lib-xrender  libraries
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libpng16.so.16 /usr/lib/x86_64-linux-gnu/libpng16.so.16
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libfontconfig.so.1 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libfreetype.so.6 /usr/lib/x86_64-linux-gnu/libfreetype.so.6
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libpixman-1.so.0 /usr/lib/x86_64-linux-gnu/libpixman-1.so.0
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libcairo.so.2 /usr/lib/x86_64-linux-gnu/libcairo.so.2
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libgomp.so.1 /usr/lib/x86_64-linux-gnu/libgomp.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0 /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libz.so.1 /usr/lib/x86_64-linux-gnu/libz.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libxcb* /usr/lib/x86_64-linux-gnu/
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libX* /usr/lib/x86_64-linux-gnu/
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libexpat.so.1 /usr/lib/x86_64-linux-gnu/libexpat.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libbrotlidec.so.1 /usr/lib/x86_64-linux-gnu/libbrotlidec.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libbrotlicommon.so.1 /usr/lib/x86_64-linux-gnu/libbrotlicommon.so.1
+COPY --from=builder /usr/lib/x86_64-linux-gnu/libbsd.so.0 /usr/lib/x86_64-linux-gnu/libbsd.so.0
 
-# **Copy the system fonts**
-COPY --from=builder /usr/share/fonts /usr/share/fonts
+ENV OMP_NESTED=TRUE
+ENV LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu

assignBarcodes.c

@@ -873,7 +873,6 @@ int print_feature_sequences(feature_arrays *features, int *total_counts, char *d
         lowerCaseDifferences(features->feature_sequences[entry->feature_index-1],annotated_sequence,feature_length);
         fprintf(feature_sequencesfp, "%3d %s %2d %7d %s\n", entry->feature_index,annotated_sequence, entry->hamming_distance,entry->counts,features->feature_names[entry->feature_index-1]);
     }
-    exit(0);
     return 0;
 }