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Update jbrowse2 4.2.1 #8263

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b697b7d
update jbrowse2
rlibouba Jun 9, 2026
52b1966
updte Jbrowse2
rlibouba Jul 31, 2026
b9217c1
update
rlibouba Jul 31, 2026
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150 changes: 87 additions & 63 deletions tools/jbrowse2/jbrowse2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,27 +131,23 @@ def metadata_from_node(node):


class JbrowseConnector(object):
def __init__(self, jbrowse, outdir, update):
def __init__(self, jbrowse, outdir, update, use_canvas_renderer=True, enable_workspaces=True, show_legends=True):
self.jbrowse = jbrowse
self.outdir = outdir
self.update = update

self.tracksToIndex = {}
self.use_canvas_renderer = use_canvas_renderer
self.enable_workspaces = enable_workspaces
self.show_legends = show_legends

# This is the id of the current assembly
self.tracksToIndex = {}
self.assembly_ids = {}

self.default_views = {}

self.plugins = []

self.use_synteny_viewer = False

self.synteny_tracks = []

self.clone_jbrowse(self.jbrowse, self.outdir)

# If upgrading, look at the existing data
self.check_existing(self.outdir)

def get_cwd(self, cwd):
Expand Down Expand Up @@ -199,7 +195,7 @@ def symlink_or_copy(self, src, dest):

def _prepare_track_style(self, xml_conf):
style_data = {
"type": "LinearBasicDisplay", # No ideal default, but should be overwritten anyway
"type": "LinearBasicDisplay", # No ideal default, but should be overwritten anyway
}

if "display" in xml_conf["style"]:
Expand All @@ -212,16 +208,13 @@ def _prepare_track_style(self, xml_conf):
return {"displays": [style_data]}

def _prepare_renderer_config(self, display_type, xml_conf):

style_data = {}

# if display_type in ("LinearBasicDisplay", "LinearVariantDisplay"):
# TODO LinearVariantDisplay does not understand these options when written in config.json
if display_type in ("LinearBasicDisplay"):
if display_type in ("LinearBasicDisplay",):

# Doc: https://jbrowse.org/jb2/docs/config/svgfeaturerenderer/
# Doc: https://jbrowse.org/jb2/docs/config/arcrenderer/
style_data["renderer"] = {
"type": "SvgFeatureRenderer",
"type": "CanvasFeatureRenderer",
"showLabels": xml_conf.get("show_labels", True),
"showDescriptions": xml_conf.get("show_descriptions", True),
"labels": {
Expand All @@ -233,36 +226,24 @@ def _prepare_renderer_config(self, display_type, xml_conf):
}

elif display_type == "LinearArcDisplay":

# Doc: https://jbrowse.org/jb2/docs/config/arcrenderer/
style_data["renderer"] = {
"type": "ArcRenderer",
"label": xml_conf.get("labels_name", "jexl:get(feature,'score')"),
"displayMode": xml_conf.get("display_mode", "arcs"),
}

elif display_type == "LinearWiggleDisplay":

wig_renderer = xml_conf.get("renderer", "xyplot")
style_data["defaultRendering"] = wig_renderer

elif display_type == "MultiLinearWiggleDisplay":

wig_renderer = xml_conf.get("renderer", "multirowxy")
style_data["defaultRendering"] = wig_renderer

elif display_type == "LinearSNPCoverageDisplay":

# Does not work
# style_data["renderer"] = {
# "type": "SNPCoverageRenderer",
# "displayCrossHatches": xml_conf.get("display_cross_hatches", True),
# }

style_data["scaleType"] = xml_conf.get("scale_type", "linear")
if "min_score" in xml_conf:
style_data["minScore"] = xml_conf["min_score"]

if "max_score" in xml_conf:
style_data["maxScore"] = xml_conf["max_score"]

Expand Down Expand Up @@ -355,6 +336,8 @@ def _load_old_synteny_views(self):

def add_assembly(self, path, label, is_remote=False, cytobands=None, ref_name_aliases=None):

label = re.sub(r"[/\\]", " ", label) # sanitize path-unsafe characters

if not is_remote:
# Find a non-existing filename for the new genome
# (to avoid colision when upgrading an existing instance)
Expand Down Expand Up @@ -663,31 +646,39 @@ def add_xam(self, parent, data, trackData, xamOpts, index=None, ext="bam", **kwa

if trackData['remote']:
rel_dest = data
# Index will be set automatically as xam url + xai .suffix by add-track cmd
else:
rel_dest = os.path.join("data", trackData["label"] + f".{ext}")
dest = os.path.join(self.outdir, rel_dest)
self.symlink_or_copy(os.path.realpath(data), dest)

if index is not None and os.path.exists(os.path.realpath(index)):
# xai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
self.subprocess_check_call(
["cp", os.path.realpath(index), dest + f".{index_ext}"]
)
else:
# Can happen in exotic condition
# e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
# => no index generated by galaxy, but there might be one next to the symlink target
# this trick allows to skip the bam sorting made by galaxy if already done outside
if os.path.exists(os.path.realpath(data) + f".{index_ext}"):
self.symlink_or_copy(
os.path.realpath(data) + f".{index_ext}", dest + f".{index_ext}"
)
else:
log.warn(
f"Could not find a bam index (.{index_ext} file) for {data}"
f"Could not find a {ext} index (.{index_ext} file) for {data}"
)

style_json = self._prepare_track_style(trackData)
track_metadata = self._prepare_track_metadata(trackData)
style_json.update(track_metadata)

self._add_track(
trackData["label"],
trackData["key"],
trackData["category"],
rel_dest,
parent,
config=style_json,
remote=trackData['remote']
)

style_json = self._prepare_track_style(trackData)

track_metadata = self._prepare_track_metadata(trackData)
Expand Down Expand Up @@ -751,19 +742,19 @@ def add_gff(self, parent, data, format, trackData, gffOpts, **kwargs):
rel_dest = os.path.join("data", trackData["label"] + ".gff")
dest = os.path.join(self.outdir, rel_dest)
rel_dest = rel_dest + ".gz"

self._sort_gff(data, dest)

style_json = self._prepare_track_style(trackData)

formatdetails = self._prepare_format_details(trackData)

style_json.update(formatdetails)

track_metadata = self._prepare_track_metadata(trackData)

style_json.update(track_metadata)

if "displays" in style_json:
for display in style_json["displays"]:
if "renderer" in display and display["renderer"]["type"] == "SvgFeatureRenderer":
display["renderer"]["type"] = "CanvasFeatureRenderer"

if gffOpts.get('index', 'false') in ("yes", "true", "True"):
if parent['uniq_id'] not in self.tracksToIndex:
self.tracksToIndex[parent['uniq_id']] = []
Expand Down Expand Up @@ -806,15 +797,16 @@ def add_gtf(self, parent, data, format, trackData, gffOpts, **kwargs):
}

style_json = self._prepare_track_style(trackData)

formatdetails = self._prepare_format_details(trackData)

style_json.update(formatdetails)

track_metadata = self._prepare_track_metadata(trackData)

style_json.update(track_metadata)

if "displays" in style_json:
for display in style_json["displays"]:
if "renderer" in display and display["renderer"]["type"] == "SvgFeatureRenderer":
display["renderer"]["type"] = "CanvasFeatureRenderer"

json_track_data.update(style_json)

self.subprocess_check_call(
Expand All @@ -834,19 +826,19 @@ def add_bed(self, parent, data, format, trackData, gffOpts, **kwargs):
rel_dest = os.path.join("data", trackData["label"] + ".bed")
dest = os.path.join(self.outdir, rel_dest)
rel_dest = rel_dest + ".gz"

self._sort_bed(data, dest)

style_json = self._prepare_track_style(trackData)

formatdetails = self._prepare_format_details(trackData)

style_json.update(formatdetails)

track_metadata = self._prepare_track_metadata(trackData)

style_json.update(track_metadata)

if "displays" in style_json:
for display in style_json["displays"]:
if "renderer" in display and display["renderer"]["type"] == "SvgFeatureRenderer":
display["renderer"]["type"] = "CanvasFeatureRenderer"

if gffOpts.get('index', 'false') in ("yes", "true", "True"):
if parent['uniq_id'] not in self.tracksToIndex:
self.tracksToIndex[parent['uniq_id']] = []
Expand Down Expand Up @@ -1339,7 +1331,7 @@ def process_annotations(self, track, parent):
parent,
dataset_path,
outputTrackConfig,
track["conf"]["options"]["synteny"]
track["conf"].get("options", {}).get("synteny", {})
)
elif dataset_ext in ("hic"):
self.add_hic(
Expand Down Expand Up @@ -1514,24 +1506,27 @@ def add_default_session(self, default_views):
with open(config_path, "r") as config_file:
config_json = json.load(config_file)

if "defaultSession" not in config_json:
config_json["defaultSession"] = {}
config_json["defaultSession"].update(session_spec)

with open(config_path, "w") as config_file:
json.dump(config_json, config_file, indent=2)

def add_general_configuration(self, data):
"""
Add some general configuration to the config.json file
Add general configuration to the config.json file, including v4.x options.
"""

config_path = os.path.join(self.outdir, "config.json")
with open(config_path, "r") as config_file:
config_json = json.load(config_file)

config_data = {}

config_data["disableAnalytics"] = data.get("analytics", "false") == "true"

config_data["workspaces"] = self.enable_workspaces
config_data["showLegends"] = self.show_legends

config_data["theme"] = {
"palette": {
"primary": {"main": data.get("primary_color", "#0D233F")},
Expand All @@ -1541,7 +1536,12 @@ def add_general_configuration(self, data):
},
"typography": {"fontSize": int(data.get("font_size", 10))},
}
config_data["useCanvasRenderer"] = data.get("use_canvas_renderer", "true") == "true"
config_data["enableWorkspaces"] = data.get("enable_workspaces", "true") == "true"
config_data["showLegends"] = data.get("show_legends", "true") == "true"

if "configuration" not in config_json:
config_json["configuration"] = {}
config_json["configuration"].update(config_data)

with open(config_path, "w") as config_file:
Expand All @@ -1566,11 +1566,9 @@ def add_plugins(self, data):

def clone_jbrowse(self, jbrowse_dir, destination):
"""
Clone a JBrowse directory into a destination directory.

Not using `jbrowse create` command to allow running on internet-less compute + to make sure code is frozen
Clone a JBrowse directory into a destination directory.
For v4.x, ensure all static files (including WebGPU/WebGL assets) are copied.
"""

copytree(jbrowse_dir, destination)
try:
shutil.rmtree(os.path.join(destination, "test_data"))
Expand Down Expand Up @@ -1626,12 +1624,19 @@ def validate_synteny(real_root):


if __name__ == "__main__":
parser = argparse.ArgumentParser(description="", epilog="")
parser = argparse.ArgumentParser(description="JBrowse2 Galaxy wrapper", epilog="")
parser.add_argument("xml", type=argparse.FileType("r"), help="Track Configuration")

parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
parser.add_argument("--update", help="Update an existing JBrowse2 instance", action="store_true")
parser.add_argument("--outdir", help="Output directory", default="out")
parser.add_argument("--use-canvas-renderer", action="store_true", default=True,
help="Use CanvasFeatureRenderer for feature tracks (recommended for v4.x).")
parser.add_argument("--enable-workspaces", action="store_true", default=True,
help="Enable tiled window management (Workspaces) in v4.x.")
parser.add_argument("--show-legends", action="store_true", default=True,
help="Show color legends in v4.x.")

args = parser.parse_args()

tree = ET.parse(args.xml.name)
Expand All @@ -1645,10 +1650,33 @@ def validate_synteny(real_root):
# be GET and not POST so it should redirect OK
GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL

use_canvas_renderer = real_root.find("metadata/general/useCanvasRenderer")
enable_workspaces = real_root.find("metadata/general/enableWorkspaces")
show_legends = real_root.find("metadata/general/showLegends")

use_canvas_renderer = (
use_canvas_renderer.text.lower() == "true"
if use_canvas_renderer is not None and use_canvas_renderer.text is not None
else args.use_canvas_renderer
)
enable_workspaces = (
enable_workspaces.text.lower() == "true"
if enable_workspaces is not None and enable_workspaces.text is not None
else args.enable_workspaces
)
show_legends = (
show_legends.text.lower() == "true"
if show_legends is not None and show_legends.text is not None
else args.show_legends
)

jc = JbrowseConnector(
jbrowse=args.jbrowse,
outdir=args.outdir,
update=args.update,
use_canvas_renderer=use_canvas_renderer if isinstance(use_canvas_renderer, bool) else (use_canvas_renderer.lower() == "true" if isinstance(use_canvas_renderer, str) else args.use_canvas_renderer),
enable_workspaces=enable_workspaces if isinstance(enable_workspaces, bool) else (enable_workspaces.lower() == "true" if isinstance(enable_workspaces, str) else args.enable_workspaces),
show_legends=show_legends if isinstance(show_legends, bool) else (show_legends.lower() == "true" if isinstance(show_legends, str) else args.show_legends),
)

# Synteny options are special, check them first
Expand Down Expand Up @@ -1750,10 +1778,6 @@ def validate_synteny(real_root):
item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
}

track_conf["style"] = {
item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
}

track_conf["style_labels"] = {
item.tag: parse_style_conf(item)
for item in (track.find("options/style_labels") or [])
Expand Down Expand Up @@ -1806,4 +1830,4 @@ def validate_synteny(real_root):
jc.add_default_session(views_for_session)
jc.add_general_configuration(general_data)
jc.add_plugins(jc.plugins)
jc.text_index()
jc.text_index()
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