Update dockerfile for version 1.4.1

containers/Dockerfile

@@ -9,6 +9,7 @@ ARG MASH_VER="v2.2"
 ARG PRODIGAL_VER="2.6.3"
 ARG MAFFT_VER="7.313"
 ARG FASTME_VER="2.1.6.1"
+ARG PANACOTA_VER="1.4.1"
 
 # re-instantiating for the app build layer
 ARG PROKKA_VER
@@ -19,6 +20,7 @@ ARG MASH_VER
 ARG PRODIGAL_VER
 ARG MAFFT_VER
 ARG FASTME_VER
+ARG PANACOTA_VER
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -55,10 +57,10 @@ RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux6
 # Install dependencies for prokka:
 # install tbl2asn manually since the one included with prokka is expired. 
 # Probably will have to do again in Dec 2021 unless Torsten removes it from prokka
-RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
-    gunzip linux64.tbl2asn.gz && \
-    mv linux64.tbl2asn /usr/bin/tbl2asn && \
-    chmod 755 /usr/bin/tbl2asn
+# RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
+#     gunzip linux64.tbl2asn.gz && \
+#     mv linux64.tbl2asn /usr/bin/tbl2asn && \
+#     chmod 755 /usr/bin/tbl2asn
 # Install prokka
 # RUN git clone https://github.com/tseemann/prokka.git
 # RUN /install_dir/prokka/bin/prokka --setupdb &&\
@@ -83,19 +85,23 @@ WORKDIR /install_dir
 # # Install bioperl
 # RUN echo yes | cpan Bio::Perl
 # # Install prokka
-RUN wget https://github.com/tseemann/prokka/archive/refs/tags/v${PROKKA_VER}.tar.gz
-RUN tar -xzf v${PROKKA_VER}.tar.gz &&\
-    rm -rf v${PROKKA_VER}.tar.gz 
-RUN /install_dir/prokka-${PROKKA_VER}/bin/prokka --setupdb &&\
-    ln -s /install_dir/prokka-${PROKKA_VER}/bin/prokka /usr/local/bin
 
-# # install tbl2asn (used by prokka)
-# RUN wget -O tbl2asn.gz https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/linux64.table2asn.gz &&\
-#     gunzip tbl2asn.gz &&\
-#     chmod +x tbl2asn &&\
-#     ln -s /install_dir/tbl2asn /usr/local/bin
-# more Examples/commands/2-Annotate.sh
-# PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
+
+
+
+# RUN wget https://github.com/tseemann/prokka/archive/refs/tags/v${PROKKA_VER}.tar.gz
+# RUN tar -xzf v${PROKKA_VER}.tar.gz &&\
+#     rm -rf v${PROKKA_VER}.tar.gz 
+# RUN /install_dir/prokka-${PROKKA_VER}/bin/prokka --setupdb &&\
+#     ln -s /install_dir/prokka-${PROKKA_VER}/bin/prokka /usr/local/bin
+
+# # # install tbl2asn (used by prokka)
+# # RUN wget -O tbl2asn.gz https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/linux64.table2asn.gz &&\
+# #     gunzip tbl2asn.gz &&\
+# #     chmod +x tbl2asn &&\
+# #     ln -s /install_dir/tbl2asn /usr/local/bin
+# # more Examples/commands/2-Annotate.sh
+# # PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
  
 
 # Install prodigal
@@ -165,11 +171,11 @@ RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
     ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
 
 # Install PanACoTA
-WORKDIR /install-dir
-RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/v1.4.0.tar.gz
-RUN tar -xzf v1.4.0.tar.gz
-WORKDIR /install-dir/PanACoTA-1.4.0
-RUN ./make
+WORKDIR /install_dir
+RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/v${PANACOTA_VER}.tar.gz
+RUN tar -xzf v${PANACOTA_VER}.tar.gz
+WORKDIR /install_dir/PanACoTA-${PANACOTA_VER}
+RUN ./make develop
 
 ENTRYPOINT ["/usr/local/bin/PanACoTA"]
 CMD ['-h']
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