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https://github.com/tom-tan/zatsu-cwl-generator
Simple CWL document generator from given execution commands
https://github.com/tom-tan/zatsu-cwl-generator
common-workflow-language commonwl cwl dlang
Last synced: 17 days ago
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Simple CWL document generator from given execution commands
- Host: GitHub
- URL: https://github.com/tom-tan/zatsu-cwl-generator
- Owner: tom-tan
- License: mit
- Created: 2019-09-13T06:31:27.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-09-07T03:33:42.000Z (over 2 years ago)
- Last Synced: 2024-10-16T13:34:27.169Z (2 months ago)
- Topics: common-workflow-language, commonwl, cwl, dlang
- Language: D
- Homepage:
- Size: 119 KB
- Stars: 4
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# zatsu-cwl-generator
[](https://github.com/tom-tan/zatsu-cwl-generator/releases/latest)
[](https://github.com/tom-tan/zatsu-cwl-generator/pkgs/container/zatsu-cwl-generator)
[](https://github.com/tom-tan/zatsu-cwl-generator/actions)
This is a simple CWL document generator from given execution commands.
# Build Requirements
- [Visual Studio Code](https://code.visualstudio.com) (optional)
- This repository provides a development environment for [Visual Studio Code Remote - Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) extension
- [D compiler](https://dlang.org/download.html)
- I confirmed with `dmd` and `ldc2` but it should work with other compilers such as `gdc`.
# How to execute
There are several ways to execute it. See `zatsu-cwl-generator --help` for more details.
- Use [Docker container](https://hub.docker.com/r/ttanjo/zatsu-cwl-generator)
```console
$ docker run --rm ghcr.io/tom-tan/zatsu-cwl-generator "cat aaa.txt bbb.txt > output.txt"
#!/usr/bin/env cwl-runner
# Generated from: cat aaa.txt bbb.txt > output.txt
class: CommandLineTool
cwlVersion: v1.0
baseCommand: cat
arguments:
- $(inputs.aaa_txt)
- $(inputs.bbb_txt)
inputs:
- id: aaa_txt
type: File
default:
class: File
location: aaa.txt
- id: bbb_txt
type: File
default:
class: File
location: bbb.txt
outputs:
- id: all-for-debugging
type:
type: array
items: [File, Directory]
outputBinding:
glob: "*"
- id: out
type: stdout
stdout: output.txt
```
- Download the latest binary from the [release page](https://github.com/tom-tan/zatsu-cwl-generator/releases/latest)
```console
$ export ver=v1.1.0
$ export os=linux # `export os=osx` for macOS
$ wget -O zatsu-cwl-generator.tar.xz https://github.com/tom-tan/zatsu-cwl-generator/releases/download/${ver}/zatsu-cwl-generator-${ver}-${os}-x86_64.tar.xz
$ tar xf zatsu-cwl-generator.tar.xz
$ chmod +x zatsu-cwl-generator
$ ./zatsu-cwl-generator "cat aaa.txt bbb.txt > output.txt"
...
```
- Use `rdmd`
```console
$ rdmd -J. zatsu-cwl-generator.d "cat aaa.txt bbb.txt > output.txt"
...
```
- Build a binary and use it
```console
$ ldc2 -J. zatsu-cwl-generator.d
$ ./zatsu-cwl-generator "cat aaa.txt bbb.txt > output.txt"
...
```
If you need a static linked binary, add `-static` to the build command:
```console
$ ldc2 -J. zatsu-cwl-generator.d # for dynamic link (default)
$ ldd zatsu-cwl-generator
/lib/ld-musl-x86_64.so.1 (0x7f476696e000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x7f4766711000)
libc.musl-x86_64.so.1 => /lib/ld-musl-x86_64.so.1 (0x7f476696e000)
$ ldc2 -J. -static zatsu-cwl-generator.d # for static link
$ ldd zatsu-cwl-generator
/lib/ld-musl-x86_64.so.1: zatsu-cwl-generator: Not a valid dynamic program
```
# How to test this program
```console
$ rdmd -J. -unittest -run zatsu-cwl-generator.d
```
# How to generate an internal document
```console
$ ldc2 -J. -Dddocs zatsu-cwl-generator.d
```
You can see a HTML file in the `docs` directory.