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comparison jbrowse2.py @ 102:099370690407 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
author fubar
date Sat, 22 Jun 2024 05:48:30 +0000
parents e4ba5f1da6ef
children 9e3f69d9fed1
comparison
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101:e4ba5f1da6ef 102:099370690407
1318 default session settings are hard and fragile. 1318 default session settings are hard and fragile.
1319 .add_default_view() and other configuration code adapted from 1319 .add_default_view() and other configuration code adapted from
1320 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py 1320 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
1321 """ 1321 """
1322 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 1322 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
1323 bpPerPx = self.bpPerPx # Browser window width is unknown and apparently cannot be figured out in JB2 code so could be 200-2000+ pixels. 1323 bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels.
1324 track_types = {} 1324 track_types = {}
1325 with open(self.config_json_file, "r") as config_file: 1325 with open(self.config_json_file, "r") as config_file:
1326 config_json = json.load(config_file) 1326 config_json = json.load(config_file)
1327 if self.config_json: 1327 if self.config_json:
1328 config_json.update(self.config_json) 1328 config_json.update(self.config_json)
1702 default_session_data["session_name"] = root.find( 1702 default_session_data["session_name"] = root.find(
1703 "metadata/general/session_name" 1703 "metadata/general/session_name"
1704 ).text 1704 ).text
1705 logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2))) 1705 logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
1706 jc.zipOut = root.find("metadata/general/zipOut").text == "true" 1706 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
1707 jc.bpPerPx = root.find("metadata/general/bpPerPx").text 1707 jc.bpPerPx = int(root.find("metadata/general/bpPerPx").text)
1708 general_data = { 1708 general_data = {
1709 "analytics": root.find("metadata/general/analytics").text, 1709 "analytics": root.find("metadata/general/analytics").text,
1710 "primary_color": root.find("metadata/general/primary_color").text, 1710 "primary_color": root.find("metadata/general/primary_color").text,
1711 "secondary_color": root.find("metadata/general/secondary_color").text, 1711 "secondary_color": root.find("metadata/general/secondary_color").text,
1712 "tertiary_color": root.find("metadata/general/tertiary_color").text, 1712 "tertiary_color": root.find("metadata/general/tertiary_color").text,