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SwarmContainer: log feedback before docker pull
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mlin committed Jan 7, 2021
1 parent d6e789d commit f75b475
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -13,7 +13,7 @@

[![PyPI version](https://img.shields.io/pypi/v/miniwdl.svg)](https://pypi.org/project/miniwdl/) `pip3 install miniwdl`

[![Anaconda-Server Badge](https://anaconda.org/conda-forge/miniwdl/badges/version.svg)](https://anaconda.org/conda-forge/miniwdl) `conda install --channel conda-forge miniwdl`
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/miniwdl/badges/version.svg)](https://anaconda.org/conda-forge/miniwdl) `conda install -c conda-forge miniwdl`

Source install: see the [Dockerfile](https://github.com/chanzuckerberg/miniwdl/blob/main/Dockerfile) for dependencies to run `setup.py`

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1 change: 1 addition & 0 deletions WDL/runtime/task_container.py
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Expand Up @@ -621,6 +621,7 @@ def resolve_tag(
image_attrs = client.images.get(image_tag).attrs
except docker.errors.ImageNotFound:
try:
logger.info(_("docker pull", tag=image_tag))
client.images.pull(image_tag)
image_attrs = client.images.get(image_tag).attrs
except docker.errors.ImageNotFound:
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6 changes: 2 additions & 4 deletions docs/getting_started.md
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Expand Up @@ -13,7 +13,7 @@ Also there is an embedded short course 'learn-miniwdl' which includes screencast

Requirements:

1. Linux or [macOS (limited support)](https://github.com/chanzuckerberg/miniwdl/issues/145)
1. GNU/Linux or [macOS (specific steps required)](https://github.com/chanzuckerberg/miniwdl/issues/145)
2. Python 3.6 or higher
3. [Docker Engine](https://docs.docker.com/install/) 17 or higher
4. Unix user must have [permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user)
Expand All @@ -22,7 +22,7 @@ Requirements:
Installation options:

* via PyPI: `pip3 install miniwdl`
* via conda: `conda install --channel conda-forge miniwdl`
* via conda: `conda install -c conda-forge miniwdl`
* see the [GitHub repo README](https://github.com/chanzuckerberg/miniwdl/) to install from source

Then open a command prompt and try,
Expand All @@ -31,8 +31,6 @@ Then open a command prompt and try,

...to test the installation with a trivial built-in workflow. This should print numerous log messages, and conclude with `miniwdl run_self_test OK` in about 30 seconds.

NOTE: On macOS, you'll first need to override the `TMPDIR` environment variable, e.g. `export TMPDIR=/tmp`, to allow Docker containers to mount shared working directories. Please [file any other issues](https://github.com/chanzuckerberg/miniwdl/issues) that arise!

## Fetch viral-pipelines

For this exercise we'll use the [Broad Institute's viral sequencing pipeline](https://github.com/broadinstitute/viral-pipelines/), which includes a small EBOV dataset for testing. Start by fetching a copy,
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