opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-11-02 19:52:14 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #6851 from martenson/backport-gie-kwds

Browse Source 
[18.05] Updated volume kwds for GIEs
This commit is contained in:
Dannon
2018-10-11 08:38:23 -04:00
committed by GitHub
parent 4a345b99c3 a1f7634fd7
commit fe6c1738c0
3 changed files with 4 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files
config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
+2 -2
View File
@@ -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,
config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
+1 -1
View File
@@ -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.
config/plugins/interactive_environments/neo/templates/neo.mako
+1 -1
View File
@@ -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.