How to install from local file?

[liezl200]

The installation of 1000genomes fails before the zip download is finished:

genepi/imputationserver-docker#5

I'm downloading the zip now to inspect why it's complaining about not finding the zip headers, but the download seems to take a few hours for 12.6 GB.

Is there a way to download the zip and then install using that local copy?

[mamanambiya]

Was there any update on this?

[lukfor]

At the moment, it is possible to install an application from the local filesystem via the install command. For example:

cloudgene install /path/to/application.zip

Moreover, it is possible to do the same using the web-interface. Open the admin-panel, click on Applications -> Install App -> from URL and enter the absolute path to you application.zip file.

[dkioroglou]

I faced the same problems as in imputationserver-docker/issues/5#issue-544815917 when I tried to install 1000 genomes phase 3 reference panel using the docker image genepi/imputationserver:v1.4.1.

I tried also to install from the local filesystem but with no luck.
Steps followed:

• Downloaded https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip
• Went to: [Admin Panel] --> [Applications] --> [Install App] --> [URL] as suggested.
• Tried the following absolute paths as URLs:
  1. http:///home/username/Downloads/1000genomes-phase3-2.0.0.zip
  2. https:///home/username/Downloads/1000genomes-phase3-2.0.0.zip
  3. file:///home/username/Downloads/1000genomes-phase3-2.0.0.zip
  4. /home/username/Downloads/1000genomes-phase3-2.0.0.zip

Any suggestions on how the URL should look like?

I haven't tried the cloudgene install. I assume that this command should be run inside docker. However, how can I access cloudgene from docker?

[ttbek]

@dkioroglou It's been a while since I did this... you might need to unzip that and point to the .yaml file for the app to install? Also, the path that you need to give it needs to be the path as it appears inside the docker container, it will be formatted like iv. So you do need to make the file available by mounting the volume when you start the docker container, something like:
-v /home/username/Downloads/:/mynewapp and then the path you would give would be where it is inside the container, so like /mynewapp/1000genomes-phase3-2.0.0.zip Maybe you can give the zip like that instead of the .yaml, I'm not sure that I tried any zipped applications.

[hanruijiang]

hi, the link is no longer available.

https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip

can you share the .zip file with me ? @liezl200 @dkioroglou @lukfor

thank you.