Help us understand the problem. What is going on with this article?

2. cromwell でCWLを実行してみる

More than 1 year has passed since last update.

cwlが実行可能はcromwellのイメージを作成する

1. cromwell でCWLを実行してみるの環境のDocker imageを作成する

cwlが実行可能なdocker imageを作成するためのDockerfile

Dockerfile
From ubuntu
MAINTAINER Percipere
RUN apt-get update
RUN apt -y upgrade
RUN apt-get -y install openjdk-8-jre
RUN apt-get -y install curl
RUN apt-get -y install python3
RUN apt-get -y install python3-pip
RUN apt-get -y install git
RUN git clone https://github.com/common-workflow-language/cwltool.git
RUN pip3 install ./cwltool 
RUN apt-get -y install vim

RUN useradd -ms /bin/bash cromwell
USER cromwell
WORKDIR /home/cromwell

RUN curl -LO https://github.com/broadinstitute/cromwell/releases/download/32/cromwell-32.jar
RUN ln -s ./cromwell-32.jar ./cromwell.jar

CMD /bin/bash

docker imageの作成

上記のDockerfileを作成したディレクトリでdocker buildを実行する

$ docker build -t cromwell .

dockerコンテナの実行

作成されたイメージをもとにcrowmellを実行する

$ docker run -it cromwell

以下はDocker内部での作業

cromwellの動作を確認

cromwell@4095de5a46e4:~$ pwd
/home/cromwell
cromwell@4095de5a46e4:~$ java -jar cromwell.jar --version
cromwell 32

cromwell でCWLを実行してみる その1
で利用したcwlのファイルを利用して、cwlのワークフローを実行
(一部省略...)

cromwell@4095de5a46e4:~$ java -jar cromwell.jar run --type cwl --inputs echo-job.yml 1st-tool.cwl 
...
[2018-05-30 08:47:57,44] [info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
{
  "outputs": {

  },
  "id": "00866459-8bbc-454c-9954-fa9f5a6548a6"
}
...
[2018-05-30 08:48:00,61] [info] Shutdown finished.

ワークフローの動作を確認

今回はここまで:smiley:

Why not register and get more from Qiita?
  1. We will deliver articles that match you
    By following users and tags, you can catch up information on technical fields that you are interested in as a whole
  2. you can read useful information later efficiently
    By "stocking" the articles you like, you can search right away
Comments
Sign up for free and join this conversation.
If you already have a Qiita account
Why do not you register as a user and use Qiita more conveniently?
You need to log in to use this function. Qiita can be used more conveniently after logging in.
You seem to be reading articles frequently this month. Qiita can be used more conveniently after logging in.
  1. We will deliver articles that match you
    By following users and tags, you can catch up information on technical fields that you are interested in as a whole
  2. you can read useful information later efficiently
    By "stocking" the articles you like, you can search right away