From 29b3c734b18e7348c76afb67543e4f02e1128675 Mon Sep 17 00:00:00 2001 From: papanikos Date: Mon, 19 Apr 2021 16:18:20 +0200 Subject: [PATCH 1/3] update marvel docker with fix --- phage-tool-Dockerfiles/MARVEL/Dockerfile | 38 ++++++++++++++++-------- 1 file changed, 26 insertions(+), 12 deletions(-) diff --git a/phage-tool-Dockerfiles/MARVEL/Dockerfile b/phage-tool-Dockerfiles/MARVEL/Dockerfile index 6b4770b..d1f5a57 100644 --- a/phage-tool-Dockerfiles/MARVEL/Dockerfile +++ b/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 \ No newline at end of file + +# Cleanup packages to reduce image size +RUN conda clean --all && apt-get autoremove From a6f8e881634c7558ca1e47c5c8c19508268e412c Mon Sep 17 00:00:00 2001 From: papanikos Date: Mon, 19 Apr 2021 16:25:08 +0200 Subject: [PATCH 2/3] include new marvel image --- configs/container.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configs/container.config b/configs/container.config index 1a01906..ab202c6 100644 --- a/configs/container.config +++ b/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-e2591bb' } 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' } From 1616aaa712b556b8d161fe1257d241a86cacc7a8 Mon Sep 17 00:00:00 2001 From: papanikos Date: Tue, 20 Apr 2021 12:04:20 +0200 Subject: [PATCH 3/3] sync image hash with commit --- configs/container.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configs/container.config b/configs/container.config index ab202c6..22ed8b9 100644 --- a/configs/container.config +++ b/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 = 'papanikos/marvel:0.2-e2591bb' } + 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' }