bhattlab/wits_workshop:classification

$ singularity pull shub://bhattlab/wits_workshop:classification

Singularity Recipe

# Metagenomics Singularity environment definition
# Eli Moss
# elimoss@stanford.edu
# January 2019
# build this environment with `sudo singularity build bhatt_meta_singularity.img bhatt_meta_singularity.def`
# for development, build with sudo singularity build --sandbox bhatt_meta_singularity bhatt_meta_singularity.def,
# and then modify with sudo singularity shell --writable bhatt_meta_singularity/
# When complete, use sudo singularity build bhatt_meta.simg bhatt_meta_singularity/

bootstrap: docker
from: neurodebian:jessie

# this command assumes at least singularity 2.3
%environment
    PATH="/usr/local/anaconda/bin:$PATH"
%post
    # install debian packages
    apt-get update
    apt-get install -y eatmydata
    eatmydata apt-get install -y wget bzip2 \
      ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 \
      git git-annex-standalone
    apt-get clean

    apt-get install -y g++ build-essential


    # install anaconda
    if [ ! -d /usr/local/anaconda ]; then
         wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
            -O ~/anaconda.sh && \
         bash ~/anaconda.sh -b -p /usr/local/anaconda && \
         rm ~/anaconda.sh
    fi
    # set anaconda path
    export PATH="/usr/local/anaconda/bin:$PATH"

    # requirements for taxonomic classification
    conda install -y -c conda-forge -c bioconda -c r \
		kraken2 krona kraken ncurses datrie r-ggplot2 r-doby r-rcolorbrewer r-scales r-plyr r-stringi

    mkdir /usr/local/anaconda/bin/taxonomy
    ktUpdateTaxonomy.sh

    #install bracken from source
    git clone https://github.com/jenniferlu717/Bracken.git
    cd Bracken
    bash install_bracken.sh
    cp -r * /usr/local/bin/


    # make /data and /scripts so we can mount it to access external resources
    if [ ! -d /data ]; then mkdir /data; fi
    if [ ! -d /scripts ]; then mkdir /scripts; fi



%runscript
    exec /bin/bash

Collection

• Name: bhattlab/wits_workshop
• License: None

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