common-workflow-language / common-workflow-language/cwltool
dockerFile
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説明
How to use dockerFile,
As I understand it works with dockerImageId, both of them has to be specified!
It would be nice to try it in some order?
- dockerImageId
- dockerPull
- dockerFile
``` yaml
requirements:
- "@import": envvar-global.cwl
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerImageId: scidap/star:v2.5.0a
dockerPull: scidap/star:v2.5.0a
dockerFile: |
#################################################################
# Dockerfile
#
# Software: STAR
# Software Version: 2.5.0a
# Description: STAR image for SciDAP
# Website: https://github.com/alexdobin/STAR, http://scidap.com/
# Provides: STAR
# Base Image: scidap/scidap:v0.0.1
# Build Cmd: docker build --rm -t scidap/star:v2.5.0a .
# Pull Cmd: docker pull scidap/star:v2.5.0a
# Run Cmd: docker run --rm scidap/star:v2.5.0a STAR
#################################################################
### Base Image
FROM scidap/scidap:v0.0.1
MAINTAINER Andrey V Kartashov "porter@porter.st"
ENV DEBIAN_FRONTEND noninteractive
################## BEGIN INSTALLATION ######################
WORKDIR /tmp
### Install STAR
ENV VERSION 2.5.0a
ENV NAME STAR
ENV URL "https://github.com/alexdobin/STAR/archive/${NAME}_${VERSION}.tar.gz"
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME}-${NAME}_${VERSION}/source && \
make -j 4 && \
cd .. && \
cp ./bin/Linux_x86_64_static/STAR /usr/local/bin/ && \
cd .. && \
strip /usr/local/bin/${NAME}; true && \
rm -rf ./${NAME}-${NAME}_${VERSION}/
```
```
/usr/local/bin/cwltool 1.0.20151126171959
Got workflow error
Traceback (most recent call last):
File "build/bdist.macosx-10.11-intel/egg/cwltool/main.py", line 159, in single_job_executor
r.run(**kwargs)
File "build/bdist.macosx-10.11-intel/egg/cwltool/job.py", line 56, in run
img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)
File "build/bdist.macosx-10.11-intel/egg/cwltool/docker.py", line 95, in get_from_requirements
if get_image(r, pull_image, dry_run):
File "build/bdist.macosx-10.11-intel/egg/cwltool/docker.py", line 21, in get_image
sp = dockerRequirement["dockerImageId"].split(":")
KeyError: 'dockerImageId'
Workflow error:
'dockerImageId'
```
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