add libncbi

containers/Dockerfile

@@ -28,10 +28,10 @@ RUN apt-get update &&\
 
 # Install packages needed and update pip
 RUN apt-get install -y \
-        wget \
-        python3 \
-        python3-pip \
-        git
+    wget \
+    python3 \
+    python3-pip \
+    git
 # Upgrade pip
 RUN pip3 install --upgrade pip
 RUN mkdir /install_dir
@@ -70,7 +70,15 @@ RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux6
 #     gunzip tbl2asn.gz &&\
 #     chmod +x tbl2asn &&\
 #     ln -s /install_dir/tbl2asn /usr/local/bin
-RUN apt-get install -y prokka
+WORKDIR /install_dir
+# RUN apt-get install -y prokka
+# RUN git clone https://github.com/tseemann/prokka.git
+# RUN prokka --dbdir /install_dir/prokka/db/ --setupdb
+# RUN prokka
+# RUN prokka --setupdb
+# RUN mv /usr/bin/prokka /usr/bin/prokka-apt
+# RUN echo "alias 'prokka'='/install_dir/prokka/bin/prokka'" > ~/.bash_aliases
+# RUN source ~/.bashrc
 
 WORKDIR /install_dir
 # RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
@@ -102,73 +110,73 @@ WORKDIR /install_dir
 # #     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
-RUN apt-get install prodigal
+
+# # Install prodigal
+# RUN apt-get install prodigal
+# # WORKDIR /install_dir
+# # RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\
+# #     tar -xzf v${PRODIGAL_VER}.tar.gz &&\
+# #     rm v${PRODIGAL_VER}.tar.gz
+# # WORKDIR /install_dir/Prodigal-${PRODIGAL_VER}
+# # RUN make 
+# # RUN make install
+
+# # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
 # WORKDIR /install_dir
-# RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\
-#     tar -xzf v${PRODIGAL_VER}.tar.gz &&\
-#     rm v${PRODIGAL_VER}.tar.gz
-# WORKDIR /install_dir/Prodigal-${PRODIGAL_VER}
-# RUN make 
-# RUN make install
-
-# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
-WORKDIR /install_dir
-RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
-    tar xvfz mmseqs-linux-sse41.tar.gz &&\
-    rm mmseqs-linux-sse41.tar.gz &&\
-    mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
-    # remove useless files
-    rm -r /install_dir/mmseqs
-
-# # Install mafft 7.313
-# RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
+# RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
+#     tar xvfz mmseqs-linux-sse41.tar.gz &&\
+#     rm mmseqs-linux-sse41.tar.gz &&\
+#     mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
+#     # remove useless files
+#     rm -r /install_dir/mmseqs
+
+# # # Install mafft 7.313
+# # RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
+# # WORKDIR /install_dir
+# # RUN wget https://mafft.cbrc.jp/alignment/software/mafft-${MAFFT_VER}-with-extensions-src.tgz &&\
+# #     tar xf mafft-7.313-with-extensions-src.tgz &&\
+# #     rm mafft-7.313-with-extensions-src.tgz
+# # WORKDIR /install_dir/mafft-7.313-with-extensions/core
+# # RUN make clean &&\
+# #     make &&\
+# #     make install
+
+# # # Install FastTree version 2.1.11 Double precision (No SSE3)
 # WORKDIR /install_dir
-# RUN wget https://mafft.cbrc.jp/alignment/software/mafft-${MAFFT_VER}-with-extensions-src.tgz &&\
-#     tar xf mafft-7.313-with-extensions-src.tgz &&\
-#     rm mafft-7.313-with-extensions-src.tgz
-# WORKDIR /install_dir/mafft-7.313-with-extensions/core
-# RUN make clean &&\
-#     make &&\
-#     make install
-
-# # Install FastTree version 2.1.11 Double precision (No SSE3)
-WORKDIR /install_dir
-RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
-    gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
-    ln -s /install_dir/FastTreeMP /usr/local/bin
+# RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
+#     gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
+#     ln -s /install_dir/FastTreeMP /usr/local/bin
 
-# Install FastME FastME 2.1.6.1
-WORKDIR /install_dir
-RUN apt-get install -y automake  &&\
-    git clone https://gite.lirmm.fr/atgc/FastME.git 
-WORKDIR /install_dir/FastME/tarball
-RUN tar xzf fastme-2.1.6.4.tar.gz &&\
-    rm fastme-2.1.6.4.tar.gz &&\
-    ln -s /install_dir/FastME/tarball/fastme-2.1.6.4/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme
-
-# Install quicktree
-WORKDIR /install_dir
-RUN git clone https://github.com/tseemann/quicktree
-WORKDIR /install_dir/quicktree
-RUN make &&\
-    ln -s /install_dir/quicktree/quicktree /usr/local/bin
+# # Install FastME FastME 2.1.6.1
+# WORKDIR /install_dir
+# RUN apt-get install -y automake  &&\
+#     git clone https://gite.lirmm.fr/atgc/FastME.git 
+# WORKDIR /install_dir/FastME/tarball
+# RUN tar xzf fastme-2.1.6.4.tar.gz &&\
+#     rm fastme-2.1.6.4.tar.gz &&\
+#     ln -s /install_dir/FastME/tarball/fastme-2.1.6.4/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme
+
+# # Install quicktree
+# WORKDIR /install_dir
+# RUN git clone https://github.com/tseemann/quicktree
+# WORKDIR /install_dir/quicktree
+# RUN make &&\
+#     ln -s /install_dir/quicktree/quicktree /usr/local/bin
 
-# Install iqtree
-WORKDIR /install_dir
-RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
-RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
-    rm iqtree-1.6.12-Linux.tar.gz &&\
-    ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+# # Install iqtree
+# WORKDIR /install_dir
+# RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
+# RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
+#     rm iqtree-1.6.12-Linux.tar.gz &&\
+#     ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
 
-# Install iqtree2
-WORKDIR /install_dir
-RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
-RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
-    rm iqtree-2.0.6-Linux.tar.gz &&\
-    ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
+# # Install iqtree2
+# WORKDIR /install_dir
+# RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
+# RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
+#     rm 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
@@ -177,5 +185,5 @@ RUN tar -xzf v${PANACOTA_VER}.tar.gz
 WORKDIR /install_dir/PanACoTA-${PANACOTA_VER}
 RUN ./make develop
 
-ENTRYPOINT ["/usr/local/bin/PanACoTA"]
-CMD ['-h']
\ No newline at end of file
+# ENTRYPOINT ["/usr/local/bin/PanACoTA"]
+# CMD ['-h']
\ No newline at end of file