Lisa2 failing to download mm2 dataset

[Rohit-Satyam]

Hi

I thought of testing out the new lisa2 version since I can not get version 1 installed. But I got the following error:

lisa multi mm10 sample_*.txt --rp_map enhanced_10K -o sample1_lisa --save_metadata
Grabbing mm10 data (~15 minutes):
	Downloading from database ...
Traceback (most recent call last):
  File "/home/subudhak/miniconda3/envs/lisa/bin/lisa", line 10, in <module>
    sys.exit(main())
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/cli/cli.py", line 475, in main
    args.func(args)
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/cli/cli.py", line 144, in lisa_multi
    lisa = FromGenes(args.species, **extract_kwargs(args, INSTANTIATION_KWARGS), log = log)
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/lisa_public_data/genes_test.py", line 78, in __init__
    super().__init__(species, _config, self.window_size, isd_method= isd_method, verbose=verbose, log=log)
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/core/lisa_core.py", line 74, in __init__
    self.data_interface = DataInterface(species, window_size=window_size, make_new=False,
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 99, in __init__
    self.download_data()
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 478, in download_data
    self.fetch_from_cistrome(self.species, self.window_size)
  File "/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 70, in fetch_from_cistrome
    os.rename(filename, cls.get_dataset_path(species, window_size))
OSError: [Errno 18] Invalid cross-device link: '/tmp/tmp80dksagu' -> '/home/subudhak/miniconda3/envs/lisa/lib/python3.9/site-packages/lisa/data/mm10_1000_2.0.h5'

Also, do you have plans for mm39 rather than mm10 now that you are already updating everything?

[dagudelov]

I am having right now the same issue. There is a conflict in the same line:

Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

Grabbing mm10 data (~15 minutes):
        Downloading from database ...
Traceback (most recent call last):
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/bin/lisa", line 8, in <module>
    sys.exit(main())
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/cli/cli.py", line 475, in main
    args.func(args)
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/cli/cli.py", line 81, in lisa_oneshot
    results, metadata = FromGenes(args.species, **extract_kwargs(args, INSTANTIATION_KWARGS)).predict(args.query_list.readlines(), **extract_kwargs(args, PREDICTION_KWARGS))
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/lisa_public_data/genes_test.py", line 78, in __init__
    super().__init__(species, _config, self.window_size, isd_method= isd_method, verbose=verbose, log=log)
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/core/lisa_core.py", line 74, in __init__
    self.data_interface = DataInterface(species, window_size=window_size, make_new=False,
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 99, in __init__
    self.download_data()
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 477, in download_data
    self.fetch_from_cistrome(self.species, self.window_size)
  File "/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/core/data_interface.py", line 70, in fetch_from_cistrome
    os.rename(filename, cls.get_dataset_path(species, window_size))
OSError: [Errno 18] Invalid cross-device link: '/tmp/tmpur2bx5c5' -> '/home/idc/daniel.agudelo/tools/apps/mamba/envs/lisa/lib/python3.9/site-packages/lisa/data/mm10_1000_2.0.h5'