higlass-manage
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higlass-manage installed via pip module not found error
I ran pip install higlass-manage
, which installed version 0.8.0 successfully. However higlass-manage view *.cool
failed with a "module not found" error for higlass.client in the view.py file. Examining the source code in view.py shows that the error occurs on the top line here:
from higlass.client import Track, View, ViewConf if datatype is None: datatype = inferred_datatype if tracktype is None and position is None: (tracktype, position) = datatype_to_tracktype(datatype) if tracktype is None: print("ERROR: Unknown track type for the given datatype:", datatype) return view = View( [ Track( track_type=tracktype, position=position, tileset_uuid=uuid, server="http://localhost:{}/api/v1/".format(port), height=200, ), ] ) viewconf = ViewConf([view]) conf = viewconf.to_dict() conf["trackSourceServers"] = [] conf["trackSourceServers"] += ["http://localhost:{}/api/v1/".format(port)] if public_data: conf["trackSourceServers"] += ["http://higlass.io/api/v1/"] # uplaod the viewconf res = requests.post( "http://localhost:{}/api/v1/viewconfs/".format(port), json={"viewconf": conf} ) if res.status_code != 200: print("Error posting viewconf:", res.status, res.content) return uid = json.loads(res.content)["uid"] # make sure this test passes on Travis CI and doesn't try to open # a terminal-based browser which doesn't return if not os.environ.get("HAS_JOSH_K_SEAL_OF_APPROVAL"): webbrowser.open( "http://localhost:{port}/app/?config={uid}".format(port=port, uid=uid) )
I see the code on github differs from this and is a newer version.
Installing directly from the github source appears to solve the problem:
pip install git+https://github.com/higlass/higlass-manage.git