Adding ViralFlye dependencies to Dockerfile

OpenOmics · May 16, 2024 · 46310a0 · 46310a0
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diff --git a/docker/nanite/Dockerfile b/docker/nanite/Dockerfile
@@ -1,15 +1,37 @@
-# Base image for metavirs,
+# Base image for nanite,
 # uses Ubuntu Jammy (LTS)
 FROM ubuntu:22.04
 
-# Depedencies of metvirs:
+# Depedencies of nanite:
 #  - nanofilt/2.8.0       # from src, installed: 2.8.0
 #      @requires: python3
 #      @requires: python3-biopython
 #      @requires: python3-pandas
 #  - minimap2/2.24        # apt-get, installed: 2.24
 #  - kronatools/2.8.1     # from src, installed: 2.8.1
 #      @requires: curl
+# Dependencies of ViralFlye:
+#  - bcftools             # apt-get bcftools/1.13-1
+#  - blast                # apt-get ncbi-blast+/2.12.0
+#  - bwa                  # apt-get bwa/0.7.17-6 
+#  - freebayes            # apt-get freebayes/1.3.6-1
+#  - minced               # install from Github: https://github.com/ctSkennerton/minced
+#  - java                 # apt-get openjdk-8-jdk, dependency of minced
+#  - prodigal             # apt-get prodigal/1:2.6.3-5
+#  - python>=3.6          # apt-get python3
+#      @requires python3-biopython
+#      @requires python3-numpy
+#      @requires python3-pysam
+#      @requires python3-scipy
+#  - samtools             # apt-get samtools/1.13-4
+#  - seqtk                # apt-get seqtk/1.3-2
+#  - tabix                # apt-get tabix/1.13
+#  - vcflib               # apt-get libvcflib-tools/1.0.3 libvcflib-dev/1.0.3
+#  - viralcomplete        # install from github: https://github.com/ablab/viralComplete
+#  - viralverify          # install from github: https://github.com/ablab/viralVerify
+#      @requires: hmmer/3.3.2
+#  - flye                 # install from github: https://github.com/fenderglass/Flye
+#  - viralFlye            # install from github: https://github.com/Dmitry-Antipov/viralFlye
 LABEL maintainer=kuhnsa@nih.gov
 
 ############### INIT ################
@@ -41,6 +63,7 @@ RUN apt-get update \
         unzip \
         wget \
         zlib1g-dev \
+        minimap2 \
         # kronatools dependencies
         curl \
         perl \
@@ -50,6 +73,22 @@ RUN apt-get update \
         python3-pip \
         python3-biopython \
         python3-pandas \
+        # ViralFlye dependencies
+        bcftools \
+        ncbi-blast+ \
+        bwa \
+        freebayes \
+        hmmer \
+        openjdk-8-jdk \
+        prodigal \
+        python3-numpy \
+        python3-pysam \
+        python3-scipy \
+        samtools \
+        seqtk \
+        tabix \
+        libvcflib-tools \
+        libvcflib-dev \
     && apt-get clean && apt-get purge \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -59,41 +98,77 @@ RUN localedef -i en_US -f UTF-8 en_US.UTF-8
 # Make python3 the default interpreter
 # and install Python Packages 
 # and install nanofilt/2.8.0
-RUN ln -sf /usr/bin/python3.8 /usr/bin/python
+RUN ln -sf /usr/bin/python3 /usr/bin/python
 RUN pip3 install --upgrade pip \
 	&& pip3 install argparse \
         && pip3 install nanofilt==2.8.0
 
-############### INSTALL ################
-# Install any bioinformatics tools
-# available with apt-get on Ubuntu/22.04
-RUN apt-get update \
-    && apt-get -y upgrade \
-    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-        # minimap2/2.24
-        minimap2 \
-        # samtools/1.13
-        samtools \
-    && apt-get clean && apt-get purge \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 ############### MANUAL ################
-# Install kronatools/v2.8.1) manually, 
-# not available to apt-get on Ubuntu/20.04.
+# Install kronatools/v2.8.1 manually, 
+# not available to apt-get on Ubuntu/22.04.
 # Dependencies already satisfied:
 # https://github.com/marbl/Krona/releases
-RUN wget https://github.com/marbl/Krona/releases/download/v2.8.1/KronaTools-2.8.1.tar \
+WORKDIR /opt2
+RUN cd /opt2 && wget https://github.com/marbl/Krona/releases/download/v2.8.1/KronaTools-2.8.1.tar \
 	    && tar -xvf KronaTools-2.8.1.tar  \
 	    && rm KronaTools-2.8.1.tar \ 
 	    && cd KronaTools-2.8.1/ \
 	    && ./install.pl
-WORKDIR /opt2
+
+# Install minced/v0.4.2 manually, 
+# not available to apt-get on Ubuntu/22.04.
+# Dependencies already satisfied:
+# https://github.com/ctSkennerton/minced/releases/tag/0.4.2
+RUN cd /opt2 && wget https://github.com/ctSkennerton/minced/archive/refs/tags/0.4.2.tar.gz \
+        && tar -xvf 0.4.2.tar.gz \
+        && rm 0.4.2.tar.gz \
+        && cd minced-0.4.2 \
+        && make \
+        && rm -rf /opt2/minced-0.4.2/t/
+
+# Install latest viralComplete manually, 
+# not available to apt-get on Ubuntu/22.04.
+# Dependencies already satisfied.
+# No relases for this program, here 
+# is the commit hash of the version: 
+# db9ffa7c1beb38c1375a33619388d4bd4d2be59b
+RUN cd /opt2 && git clone https://github.com/ablab/viralComplete.git /opt2/viralComplete \
+    && cd /opt2/viralComplete \
+    && git checkout db9ffa7c1beb38c1375a33619388d4bd4d2be59b \
+    && chmod -R a+rX /opt2/viralComplete/bin
+
+# Install latest viralVerify manually,
+# not available to apt-get on Ubuntu/22.04.
+# Dependencies already satisfied.
+# No releases for latest program, here 
+# is the commit hash of the version: 
+# 4a425c88662a67c9301a3a14e7e4f78a4e115d4d
+RUN cd /opt2 && git clone https://github.com/ablab/viralVerify.git /opt2/viralVerify \
+    && cd /opt2/viralVerify \
+    && git checkout 4a425c88662a67c9301a3a14e7e4f78a4e115d4d \
+    && chmod -R a+rX /opt2/viralComplete/bin
+
+# Install flye/2.9.4 manually,
+# not available to apt-get on Ubuntu/22.04.
+# Dependencies already satisfied.
+RUN cd /opt2 && wget https://github.com/fenderglass/Flye/archive/refs/tags/2.9.4.tar.gz \
+    && tar -xvf 2.9.4.tar.gz \
+    && rm 2.9.4.tar.gz \
+    && cd Flye-2.9.4 \
+    && python3 setup.py install
+
+# Install viralFlye/0.2 manually,
+# not available to apt-get on Ubuntu/22.04.
+# Dependencies already satisfied.
+RUN cd /opt2 && wget https://github.com/Dmitry-Antipov/viralFlye/archive/refs/tags/v0.2.tar.gz \
+    && tar -xvf v0.2.tar.gz \
+    && rm v0.2.tar.gz 
 
 ################ POST #################
 # Add Dockerfile and export environment 
 # variables and set java8 as default with links
 # to alternative versions
 ADD Dockerfile /opt2/nanite.dockerfile
 RUN chmod -R a+rX /opt2
-ENV PATH="/opt2:$PATH"
+ENV PATH="/opt2:/opt2/minced-0.4.2:/opt2/viralComplete/bin:/opt2/viralVerify/bin:/opt2/viralFlye-0.2:$PATH"
 WORKDIR /data2
diff --git a/docker/nanite/README.md b/docker/nanite/README.md
@@ -7,20 +7,20 @@ Directly below are instructions for building an image using the provided Dockerf
 docker image ls
 
 # Build from Dockerfile
-docker build --no-cache -f Dockerfile --tag=nanite:v0.1.0 .
+docker build --no-cache -f Dockerfile --tag=nanite:v0.2.0 .
 
 # Testing, take a peek inside
-docker run -ti nanite:v0.1.0 /bin/bash
+docker run -ti nanite:v0.2.0 /bin/bash
 
 # Updating Tag  before pushing to DockerHub
-docker tag nanite:v0.1.0 skchronicles/nanite:v0.1.0
-docker tag nanite:v0.1.0 skchronicles/nanite         # latest
+docker tag nanite:v0.2.0 skchronicles/nanite:v0.2.0
+docker tag nanite:v0.2.0 skchronicles/nanite         # latest
 
 # Check out new tag(s)
 docker image ls
 
 # Push new tagged image to DockerHub
-docker push skchronicles/nanite:v0.1.0
+docker push skchronicles/nanite:v0.2.0
 docker push skchronicles/nanite:latest
 ```
 
@@ -29,7 +29,7 @@ docker push skchronicles/nanite:latest
 Scan your image for known vulnerabilities:
 
 ```bash
-docker scan nanite:v0.1.0
+docker scan nanite:v0.2.0
 ```
 
 > **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.