Merge pull request #134 from papanikos/marvel_update

Marvel updated container

configs/container.config

@@ -6,7 +6,7 @@ process {
     withLabel: emboss           { container = ' nanozoo/emboss:6.6.0--418c521' }
     withLabel: ggplot2          { container = 'nanozoo/r_ggplot2:0.1--6405f6d' }
     withLabel: hmmscan          { container = 'nanozoo/hmmer:3.3--3db9dd1' }
-    withLabel: marvel           { container = 'multifractal/marvel:0.1' }
+    withLabel: marvel           { container = 'papanikos/marvel:0.2-29b3c73' }
     withLabel: metaphinder      { container = 'multifractal/metaphinder:0.1' }
     withLabel: pprmeta          { container = 'multifractal/ppr-meta:0.3.1' }
     withLabel: prodigal         { container = 'nanozoo/prodigal:2.6.3--2769024' }

phage-tool-Dockerfiles/MARVEL/Dockerfile

@@ -1,23 +1,37 @@
-FROM ubuntu:bionic
+FROM continuumio/miniconda3:latest
 
-RUN apt update && apt install -y wget ncbi-blast+ procps hmmer git python3 python3-pip \
-    libdatetime-perl libxml-simple-perl libdigest-md5-perl default-jre bioperl && \
-    git clone https://github.com/LaboratorioBioinformatica/MARVEL && \
-    git clone https://github.com/tseemann/prokka.git && \
-    pip3 install -U numpy scipy biopython scikit-learn
+RUN apt-get update && apt-get upgrade -y && apt-get install -y procps
 
-RUN cpan Bio::Perl
+RUN conda config --add channels conda-forge && \
+	conda config --add channels defaults && \
+    conda config --add channels bioconda
+
+# Install all dependencies with conda
+RUN conda install -y \
+    python=3.7 \
+    hmmer \
+    biopython=1.75 \
+    scikit-learn=0.19.1 \
+    numpy \
+    prokka \
+    scipy
+
+# TEMPORARY: Use this branch with the fix from thr fork
+RUN git clone https://github.com/papanikos/MARVEL.git -b fix_1 
 
 WORKDIR /MARVEL/
+# Get the data
 RUN python3 download_and_set_models.py
 # small hack due to stupid database pathing
 RUN sed -i 's#models/#/MARVEL/models/#g' marvel_bins.py
+#Make the script executable
 RUN chmod +x /MARVEL/marvel_bins.py
+
+# Go back to root dir
 WORKDIR /
 
+# Include the executable marvel_bins.py in the PATH
 ENV PATH /MARVEL:$PATH 
-ENV PATH /prokka/bin:$PATH 
-# remove old versions from previous blast install (biopython/perl) and do a fresh install
-RUN rm /usr/bin/makeblastdb && rm /usr/bin/blast* && apt install ncbi-blast+ && \
-    apt remove -y git python3-pip && apt-get clean &&  rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-RUN prokka --setupdb
+
+# Cleanup packages to reduce image size
+RUN conda clean --all && apt-get autoremove