From 1b04ba3833597f2ebdc2e4f527044906ab7a4e7d Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 4 Feb 2016 11:02:11 +0100 Subject: [PATCH] use bioblend for dataset import instead of mount --- .../phinch/templates/phinch.mako | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/config/plugins/interactive_environments/phinch/templates/phinch.mako b/config/plugins/interactive_environments/phinch/templates/phinch.mako index e6308f6f0a7..3b139ba311d 100644 --- a/config/plugins/interactive_environments/phinch/templates/phinch.mako +++ b/config/plugins/interactive_environments/phinch/templates/phinch.mako @@ -6,15 +6,12 @@ import os # Sets ID and sets up a lot of other variables ie_request.load_deploy_config() -# Define a volume that will be mounted into the container. -# This is a useful way to provide access to large files in the container, -# if the user knows ahead of time that they will need it. -user_file = ie_request.volume(hda.file_name, '/home/Phinch/data/'+os.path.basename(hda.file_name)+'.biom', how='ro') # Launch the IE. This builds and runs the docker command in the background. -ie_request.launch( - volumes=[user_file] -) +ie_request.launch(env_override={ + 'dataset_hid': hda.hid, + 'dataset_filename': hda.file_name +}) # Only once the container is launched can we template our URLs. The ie_request # doesn't have all of the information needed until the container is running.