kenichi

FROM google/cloud-sdk:latest

ARG UID
ARG GID
ARG USERNAME

RUN useradd -u $UID -g $GID $USERNAME
WORKDIR /home/$USERNAME
USER $USERNAME

kenichi

defmodule KEx do
  @moduledoc "custom IEx extensions"

  @doc """
  Send data to `pbcopy`, a macOS utility that reads STDIN into the clipboard.
  """
  def pbcopy(data) do
    port = Port.open({:spawn, "/usr/bin/pbcopy"}, [:binary])
    send(port, {self(), {:command, data}})
    send(port, {self(), :close})

kenichi

FROM elixir:1.13-alpine AS base

RUN apk add --no-cache \
    bash \
    inotify-tools \
    nodejs npm \
    openssl

WORKDIR /app
CMD ["mix", "phx.server"]

kenichi

$ bionode-ncbi search assembly phylos | jq .uid
"874841"

$ bionode-ncbi download assembly 874841

$ cd 874841/

$ gunzip GCA_001865755.1_ASM186575v1_genomic.fna.gz

$ head GCA_001865755.1_ASM186575v1_genomic.fna 

kenichi

$ prefetch SRS4167515
prefetch.2.9.3: 1) Downloading 'SRS4167515'...
prefetch.2.9.3:  Downloading via https...
prefetch.2.9.3: 1) 'SRS4167515' was downloaded successfully
prefetch.2.9.3: 'SRS4167515' has 0 unresolved dependencies

kenichi

 $ head SRS4167515_?.fastq
==> SRS4167515_1.fastq <==
@SRS4167515.1 1 length=76
AGTCTTGTCTCCCAGCAACAATCCGAAACCACCATCTCAATGGAAGAGGCTTCTTTCCCAGAACCTCCTCCACTTG
+SRS4167515.1 1 length=76
AAAAAAE///EAE/E</EAEA/A/EAEEEE/EAEE<EEE<E//EEEA//EEAEEA///E//EAEE/E/EAAEEEE/
@SRS4167515.2 2 length=76
GTCTTGTCTCCCAAGCAACAAGCCGAAACCACCATCTCAATGGAAGAGGCTTCTTTCCCAGACCCTCCTCCACTTG
+SRS4167515.2 2 length=76
AAAAAEEEEEEEEEEEEEEE6EEEEEEEEE/EE/EEEEE6EEEEEEEEEEEAEEAEEEAEE66EEEAEEA<AAAEE

kenichi

$ fastq-dump --split-files SRS4167515.sra 
Read 2840859 spots for SRS4167515.sra
Written 2840859 spots for SRS4167515.sra

kenichi

ncbi/
└── public
    └── sra
        └── SRS4167515.sra

kenichi

FROM base_prod_example_php_fpm:latest

COPY --chown=www-data example /var/www/example/

kenichi

FROM local_example_php_fpm:latest

COPY --chown=www-data \
     example/composer.json \
     example/composer.lock \
     example/composer.phar \
     /var/www/example/
COPY --chown=www-data example/vendor /var/www/example/vendor