Merge pull request #6840 from thobalose/volume

Updated volume kwds.
galaxyproject · Oct 10, 2018 · f41128a · f41128a
2 parents c9b0379 + 6c580b8
commit f41128a
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Showing 3 changed files with 4 additions and 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
@@ -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
@@ -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
@@ -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.