diff --git a/scripts/process_collections.py b/scripts/process_collections.py index 0937d36..9f72c5d 100644 --- a/scripts/process_collections.py +++ b/scripts/process_collections.py @@ -208,7 +208,7 @@ def process_collections(self, cmds_only, mode): project_id = ".".join(bw_name.split(".")[1:-2]) # cmd = f'jbrowse add-track {bw_name} --assemblyNames {name} --out {os.path.abspath(self.out_dir)} --load copy --force' - cmd = f"jbrowse add-track {url} --name {bw_id[0]} --assemblyNames {parent[0]} --out {os.path.abspath(self.out_dir)} --force" + cmd = f"jbrowse add-track {url} --name {bw_id[0]} --assemblyNames {parent[0]} --category expression,{project_id} --out {os.path.abspath(self.out_dir)} --force" #cmd = f"jbrowse add-track {self.from_github}/{genus}/{species}/expression/{project_id}/{bw_name} --name {bw_id[0]} --assemblyNames {parent[0]} --load copy --out {os.path.abspath(self.out_dir)} --force" """ dis_name = self.files[collection_type][dsfile].get( @@ -705,14 +705,14 @@ def add_collections(self, collection_type, genus, species): ), # url encode for .yml file and Jekyll linking "description": "JBrowse2 Linear Genome View", } # the object that will be written into the .yml file - + print(f"linear data: {linear_data}") if strain_lookup not in self.infraspecies_resources: self.infraspecies_resources[strain_lookup] = ( [] ) # initialize infraspecies list within species if self.jbrowse_url: # dont add data if no jbrowse url set self.infraspecies_resources[strain_lookup].append(linear_data) - + logger.debug(f"linear data for bw: {linear_data} \n") ###