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README: some fixes
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mr-c committed Jun 26, 2024
1 parent 2762c45 commit 7130c17
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -12,7 +12,7 @@ RUN apt-get update && \
sh -c 'echo deb https://oss-binaries.phusionpassenger.com/apt/passenger buster main > /etc/apt/sources.list.d/passenger.list'

RUN apt-get update && \
apt-get install -y --no-install-recommends passenger python3-setuptools build-essential python3-dev python3-pip git && \
apt-get install -y --no-install-recommends passenger python3-setuptools build-essential python3-dev python3-pip python3-wheel git && \
pip3 install pip==21.1.3

RUN apt-get install -y --no-install-recommends libcurl4-openssl-dev libssl-dev
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8 changes: 5 additions & 3 deletions README.md
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Expand Up @@ -5,7 +5,7 @@ Execution Service](https://github.com/ga4gh/workflow-execution-schemas) 1.0.0 AP

It provides [Arvados](https://arvados.org/) and [Toil](http://toil.ucsc-cgl.org/) backends. It
also works with any `cwl-runner` that supports the CWL standard command line
interface: http://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts
interface: <http://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts>

## Installation:

Expand Down Expand Up @@ -42,7 +42,9 @@ $ wes-client --info
Attachments must be accessible from the filesystem. Workflow runners may also support http URLs or other storage systems.

```
$ wes-client --attachments="testdata/dockstore-tool-md5sum.cwl,testdata/md5sum.input" testdata/md5sum.cwl testdata/md5sum.cwl.json
$ wes-client --host localhost:8080 --proto http \
--attachments="testdata/dockstore-tool-md5sum.cwl,testdata/md5sum.input" \
testdata/md5sum.cwl testdata/md5sum.cwl.json
```

### List workflows
Expand Down Expand Up @@ -89,7 +91,7 @@ $ wes-server --backend=wes_service.toil_wes --opt extra=--clean=never

```
$ pip install cwltool
$ wes-server --backend=wes_service.cwl_runner --opt runner=cwltool --opt extra=--logLevel=CRITICAL
$ wes-server --backend=wes_service.cwl_runner --opt runner=cwltool --opt extra=--debug
```

### Pass parameters to cwl-runner
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2 changes: 1 addition & 1 deletion wes-docker.sh
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@@ -1,6 +1,6 @@
#!/bin/sh
set -ex
python setup.py sdist
make dist
docker build --build-arg version=4.0 --build-arg arvversion=2.2.1 -t commonworkflowlanguage/workflow-service .
docker run -ti -p 127.0.0.1:3000:3000/tcp \
-v$PWD/config.yml:/var/www/wes-server/config.yml \
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