diff --git a/docker/metavirs/Dockerfile b/docker/metavirs/Dockerfile index 5e53c87..025b796 100644 --- a/docker/metavirs/Dockerfile +++ b/docker/metavirs/Dockerfile @@ -18,8 +18,7 @@ FROM ubuntu:20.04 # - seqtk/1.3 # apt-get, deafult: 1.3 # - spades/3.15.4 # from src, installed: 3.15.4 # - ucsc/418 # personal mirror: snapshot Nov 2nd, 2020 -# - blastn/2.13.0+ # download binary, installed: 2.13.0+ -# - fastx_toolkit/0.0.13 # download binary, installed: 0.0.13 +# - taxonkit/0.18.0 # download binary, installed: 0.18.0 LABEL maintainer=kuhnsa@nih.gov ############### INIT ################ @@ -230,34 +229,26 @@ WORKDIR /opt2 # Install spades/3.15.4 manually, latest version # not available to apt-get on Ubuntu/20.04. -# Dependencies already satisfied: -RUN wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz \ +# Not longer available at http://cab.spbu.ru, +# must be downloaded from Github release. +# Dependencies already satisfied. +RUN wget https://github.com/ablab/spades/releases/download/v3.15.4/SPAdes-3.15.4-Linux.tar.gz \ && tar -xvzf SPAdes-3.15.4-Linux.tar.gz \ && rm /opt2/SPAdes-3.15.4-Linux.tar.gz # Add metaspades to $PATH ENV PATH="/opt2/SPAdes-3.15.4-Linux/bin:$PATH" WORKDIR /opt2 -# Install blastn/2.13.0+ from NCBI FTP, -# not available to apt-get on Ubuntu/20.04. -# Dependencies already satisfied: -RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz \ - && tar -zvxf ncbi-blast-2.13.0+-x64-linux.tar.gz ./ncbi-blast-2.13.0+/bin/blastn \ - && rm ncbi-blast-2.13.0+-x64-linux.tar.gz -# Add blastn to $PATH -ENV PATH="/opt2/ncbi-blast-2.13.0+/bin:$PATH" -WORKDIR /opt2 - -# Install fastx_toolkit/0.0.13 from CSHL, +# Install taxonkit/0.18.0 # not available to apt-get on Ubuntu/20.04. -# Dependencies already satisfied: -RUN mkdir fastx_toolkit \ - && cd fastx_toolkit \ - && wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 \ - && tar -jvxf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 ./bin/fastq_to_fasta \ - && rm fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 -# Add fastq_to_fasta to $PATH -ENV PATH="/opt2/fastx_toolkit/bin:$PATH" +# Dependencies already satisfied +RUN mkdir taxonkit-0.18.0 \ + && cd taxonkit-0.18.0 \ + && wget https://github.com/shenwei356/taxonkit/releases/download/v0.18.0/taxonkit_linux_amd64.tar.gz \ + && tar -zvxf taxonkit_linux_amd64.tar.gz \ + && rm taxonkit_linux_amd64.tar.gz +# Add taxonkit to $PATH +ENV PATH="/opt2/taxonkit-0.18.0:$PATH" WORKDIR /opt2 ################ POST #################