# HG changeset patch # User yating-l # Date 1482966242 18000 # Node ID d16f22205ff7a48467a1113d6bee625e9cd27661 # Parent 095cc9f68adf4a93319abb8b1396e442b52db580 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty diff -r 095cc9f68adf -r d16f22205ff7 trackHub/README.md --- a/trackHub/README.md Wed Dec 28 17:56:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -This folder exists to configure Galaxy to handle the files generated by HubArchiveCreator tool - -* The **content** of datatypes_conf.xml should go inside config/datatypes_conf.xml, under \ (Copy config/datatypes_conf.xml.sample to config/datatypes_conf.xml if it does not exist yet) -* The content of tracks_partial.py should go inside `lib/galaxy/datatypes/tracks.py` -* trackhub.xml should go inside display_application/ucsc/ - - -TODO: - -- [x] Create a script to copy all these files directly into galaxy => Done but not usable now I have changed the datatype to match Galaxy IUC -- [ ] Need to modify the script `util/add_datatype.py` to match the changes introduced in https://github.com/galaxyproject/galaxy/pull/2348 -- [x] Create a package in ToolShed that install directly this when installing HubArchiveCreator => Not recommended by Galaxy IUC and team diff -r 095cc9f68adf -r d16f22205ff7 trackHub/datatypes_conf.xml --- a/trackHub/datatypes_conf.xml Wed Dec 28 17:56:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ - - - diff -r 095cc9f68adf -r d16f22205ff7 trackHub/trackhub.xml --- a/trackHub/trackhub.xml Wed Dec 28 17:56:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=${qp($hub_file.url + '/myHub/hub.txt')}&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on - - - diff -r 095cc9f68adf -r d16f22205ff7 trackHub/tracks_partial.py --- a/trackHub/tracks_partial.py Wed Dec 28 17:56:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -""" -HubAssembly datatype -""" -import logging - -from galaxy.datatypes.text import Html - -log = logging.getLogger( __name__ ) - -# !!! README !!! The content of this file should be added in tracks.py, but do it carefully! -# Don't erase the existing content - - -class UCSCTrackHub( Html ): - """ - derived class for BioC data structures in Galaxy - """ - - file_ext = 'trackhub' - composite_type = 'auto_primary_file' - - def __init__( self, **kwd ): - Html.__init__( self, **kwd ) - - def generate_primary_file( self, dataset=None ): - """ - This is called only at upload to write the html file - cannot rename the datasets here - they come with the default unfortunately - """ - rval = [ - 'Files for Composite Dataset (%s)

\ - This composite dataset is composed of the following files:

') - return "\n".join(rval) - - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub" - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "Track Hub structure: Visualization in UCSC Track Hub" - - def sniff( self, filename ): - return False