VirFinder 개요

FROM rocker/verse:3.6.0
MAINTAINER YOHEI_KUMAGAI

# R

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    lbzip2 \
    libfftw3-dev \
    libgdal-dev \
    libgeos-dev \
    libgsl0-dev \
    libgl1-mesa-dev \
    libglu1-mesa-dev \
    libhdf4-alt-dev \
    libhdf5-dev \
    libjq-dev \
    liblwgeom-dev \
    libpq-dev \
    libproj-dev \
    libprotobuf-dev \
    libnetcdf-dev \
    libsqlite3-dev \
    libssl-dev \
    libudunits2-dev \
    netcdf-bin \
    postgis \
    protobuf-compiler \
    sqlite3 \
    tk-dev \
    wget \
    unixodbc-dev \
  && install2.r --error \
    RColorBrewer \
    RandomFields \
    RNetCDF \
    classInt \
    deldir \
    gstat \
    hdf5r \
    lidR \
    mapdata \
    maptools \
    mapview \
    ncdf4 \
    proj4 \
    raster \
    rgdal \
    rgeos \
    rlas \
    sf \
    sp \
    spacetime \
    spatstat \
    spatialreg \
    spdep \
    geoR \
    geosphere \
    vegan \
    dichromat \
    ## from bioconductor
    && R -e "BiocManager::install(c('rhdf5','qvalue'))" \ # ここからVirSorterのインストール、ただしrhdf5はVirSorter関係ない
    && R -e "install.packages(\"glmnet\", dependencies=TRUE)" \
    && R -e "install.packages(\"Rcpp\", dependencies=TRUE)"
WORKDIR /root
RUN git clone https://github.com/jessieren/VirFinder.git
RUN R CMD INSTALL /root/VirFinder/linux/VirFinder_1.1.tar.gz

동작 확인

(base) [kumay@at028 VirFinder]$ module load singularity
(base) [kumay@at028 VirFinder]$ singularity exec ~/test_container/r-for-metagenome-latest.img R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(VirFinder)
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-18

Loading required package: qvalue
> predResult <- VF.pred("Input_contigs.fna")
[1] "Input_contigs.fna [1] line1-3 k141_2 flag=1 multi=2.0000 len=336 len 336 score 0.9184 pvalue 0.01"
[1] "Input_contigs.fna [2] line3-5 k141_3 flag=1 multi=1.0000 len=328 len 328 score 0.7846 pvalue 0.0494"
[1] "Input_contigs.fna [3] line5-7 k141_4 flag=1 multi=7.0000 len=303 len 303 score 0.6339 pvalue 0.1167"
...

library(VirFinder)
setwd("/home/kumay/virus_data/VirFinder")
predResult <- VF.pred("Input_contigs.fna")
predResult$qvalue <- VF.qvalue(predResult$pvalue)
write(predResult[order(predResult$qvalue),],file="predicted_virus_sorted_by_qvalues")