proteowizard/panorama-files repository overview

Simple Docker image which will download and upload files to a Panorama Server⁠ such as PanoramaWeb⁠.

⁠Source

The source code for this repository is available at https://github.com/uw-maccosslab/panorama-examples/tree/master/docker/panorama-files⁠

⁠Building the docker image

To build the docker image, simply run

docker image build -t panorama-files:1.0 .

⁠Using the docker image

⁠Setup

To use the docker image, you will need to configure a .netrc file to contain the credentials for you Panorama server. A netrc file (.netrc or _netrc) is used to hold credentials necessary to login to your LabKey Server and authorize access to data stored there. The netrc file contains configuration and autologin information when using APIs. It may be used when working with SAS Macros, Transformation Scripts in Java or using the Rlabkey package.

To create the .netrc file, follow the instructions on the Create a netrc file⁠ documentation.

⁠Download a file

Below is an example of how you can download a file from your Panorama server

docker run -it -v $HOME/.netrc:/root/.netrc:ro -v $PWD:/data --rm panorama-files:1.0 python /maccoss/download_file.py --url https://panoramaweb.org/_webdav/home/Example Data/Workflow/%40files/Study9S_Site20_v2.sky

The file Study9S_Site20_v2.sky will be downloaded to the current working directory.

⁠Upload a file

Below is an example for howto upload a file to your Panorama server

docker run -it -v $HOME/.netrc:/root/.netrc:ro -v $PWD:/data --rm panorama-files:1.0 python /maccoss/upload_file.py --url https://panoramaweb.org --folder home/Example Data/Workflow --experiment run_skyline --file-name Site20_STUDY9S_Cond_6ProtMix_QC_01.sky.zip

The file Site20_STUDY9S_Cond_6ProtMix_QC_01.sky.zip will be uploaded to the folder https://panoramaweb.org/home/Example⁠ Data/Workflow/project-begin.view

⁠Downloading the Docker image

This docker repo is available on Docker Hub at https://hub.docker.com/repository/docker/proteowizard/panorama-files/general⁠

It can be downloaded by running

docker pull proteowizard/panorama-files:1.0