From a1f7634fd7dca45902a2d3f67d2279db3aa2270d Mon Sep 17 00:00:00 2001 From: thobalose Date: Tue, 9 Oct 2018 13:22:55 +0200 Subject: [PATCH] Updated volume kwds. --- .../bam_iobio/templates/bam_iobio.mako | 4 ++-- .../hicbrowser/templates/hicbrowser.mako | 2 +- .../plugins/interactive_environments/neo/templates/neo.mako | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako b/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako index e456e83b48d..16115b2847a 100644 --- a/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako +++ b/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako @@ -9,8 +9,8 @@ ie_request.load_deploy_config() ie_request.attr.docker_port = 80 ie_request.attr.import_volume = False -bam = ie_request.volume(hda.file_name, '/input/bamfile.bam', how='ro') -bam_index = ie_request.volume(hda.metadata.bam_index.file_name, '/input/bamfile.bam.bai', how='ro') +bam = ie_request.volume(hda.file_name, '/input/bamfile.bam', mode='ro') +bam_index = ie_request.volume(hda.metadata.bam_index.file_name, '/input/bamfile.bam.bai', mode='ro') ie_request.launch(volumes=[bam, bam_index], env_override={ 'PUB_HTTP_PORT': ie_request.attr.galaxy_config.dynamic_proxy_bind_port, diff --git a/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako b/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako index 2c0bf9564b1..cf69cc8f633 100644 --- a/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako +++ b/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako @@ -9,7 +9,7 @@ import os mount_path = hda.file_name - data_vol = ie_request.volume(mount_path, '/data/data_pack.tar.gz', how='rw') + data_vol = ie_request.volume(mount_path, '/data/data_pack.tar.gz', mode='rw') # Add all environment variables collected from Galaxy's IE infrastructure # Launch the IE. diff --git a/config/plugins/interactive_environments/neo/templates/neo.mako b/config/plugins/interactive_environments/neo/templates/neo.mako index 0ed4be71b35..c1df7807375 100644 --- a/config/plugins/interactive_environments/neo/templates/neo.mako +++ b/config/plugins/interactive_environments/neo/templates/neo.mako @@ -7,7 +7,7 @@ # if the user knows ahead of time that they will need it. import os mount_path = str(os.path.dirname(hda.file_name)) + '/dataset_{}_files'.format( hda.dataset.id ) - data_vol = ie_request.volume(mount_path, '/data', how='rw') + data_vol = ie_request.volume(mount_path, '/data', mode='rw') # data_vol = ie_request.volume('${HOME}/neo4j/data', '/data/', how='rw') # Add all environment variables collected from Galaxy's IE infrastructure # Launch the IE.