higlass-manage browser

[faryabib]

I'm trying to follow HiGlass documentation to locally setup HiGlass on a workstation with a static IP address, then use my desktop to view the data. "higlass-manage ingest" moves the test file sample.mcool to the default directory /tmp/higlass-docker/sample.mcool on the workstation. From the desktop, I can load the HiGlass browser (Workstation_IP:8888/app), and view the list of public data sets, but not the local data sample.mcool.

Also following the higlass-manage usage fails as shown here:

wget https://s3.amazonaws.com/pkerp/public/hic-resolutions.cool
sudo higlass-manage view hic-resolutions.cool
state True
temp_dir: /tmp/higlass-docker
Inferred filetype: cooler
Inferred datatype: matrix
state True
Inferred datatype: matrix
state True
state True
name_text:
hg_name: default
command: python higlass-server/manage.py ingest_tileset --filename /tmp/hic-resolutions.cool --filetype cooler --datatype matrix --uid Bz-gWBMMR1SMa6uvx6h9HA
Traceback (most recent call last):
File "/usr/local/bin/higlass-manage", line 8, in
sys.exit(cli())
File "/usr/lib/python3/dist-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.8/dist-packages/higlass_manage/view.py", line 157, in view
from higlass.client import Track, View, ViewConf
ModuleNotFoundError: No module named 'higlass'

[pkerpedjiev]

Hi! Could you try running the following?

pip install higlass-python
higlass-manage view hic-resolutions.cool

[faryabib]

Thanks. It worked. But, I thought the whole idea of having a container is to not install packages separately.

[pkerpedjiev]

Yeah, that's right. But since we have a lot of moving parts it's a little more complicated. The higlass-manage package is a Python package that serves as a wrapper around the Docker container. So you end up having to install much fewer packages. The missing dependency here was a big that should be fixed in the latest version. I hope the helps! Please don't hesitate to reach out with any other issues. I should also mention that we've been experimenting with a hosted HiGlass instance that requires no installation. You can see a demo at resgen.io/paper-data. Fell free to shoot me an email if you're interested in trying it out.

…

On Fri, Jun 5, 2020, 5:33 AM R. Babak Faryabi ***@***.***> wrote: Thanks. It worked. But, I thought the whole idea of having a container is to not install packages separately. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#60 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQLLDIRESIDYWBXP77A56LRVDQY3ANCNFSM4NTCM4DQ> .

[bskubi]

I was having a similar issue:

higlass-manage view demo.contact_matrix.cool
Pulling latest image...
done
Data directory: /home/benjamin/hg-data
Temp directory: ()
Starting... default 8989
Docker started: higlass-manage-container-default
sending request 1
Waiting to start (tilesets)...
sending request 2
Waiting to start (tilesets)...
sending request 3
Waiting to start (tilesets)...
sending request 4
Non 200 status code returned (502), waiting...
sending request 5
Non 200 status code returned (502), waiting...
sending request 6
Non 200 status code returned (502), waiting...
sending request 7
Non 200 status code returned (502), waiting...
sending request 8
Non 200 status code returned (502), waiting...
sending request 9
public_data: True
Replaced js file
Started
Inferred filetype: cooler
Inferred datatype: matrix
state True
Inferred datatype: matrix
state True
state True
name_text:
hg_name: default
command: python higlass-server/manage.py ingest_tileset --filename /tmp/demo.contact_matrix.cool --filetype cooler --datatype matrix --uid dNmr82z4TOuMzOQYf7yGDQ
Traceback (most recent call last):
File "/home/benjamin/anaconda3/bin/higlass-manage", line 8, in
sys.exit(cli())
^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/higlass_manage/view.py", line 157, in view
from higlass.client import Track, View, ViewConf
ModuleNotFoundError: No module named 'higlass'

After running pip install higlass-python I tried viewing my .cool file again:

higlass-manage view demo.contact_matrix.cool
state True
temp_dir: /tmp/higlass-docker
Inferred filetype: cooler
Inferred datatype: matrix
Traceback (most recent call last):
File "/home/benjamin/anaconda3/bin/higlass-manage", line 8, in
sys.exit(cli())
^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/benjamin/anaconda3/lib/python3.11/site-packages/higlass_manage/view.py", line 157, in view
from higlass.client import Track, View, ViewConf
ModuleNotFoundError: No module named 'higlass.client'

Any idea where this error is coming from?

[Gon1976]

I have the same error after install higlass-python
higlass-manage view hic-resolutions.cool
state True
temp_dir: /tmp/higlass-docker
Inferred filetype: cooler
Inferred datatype: matrix
Traceback (most recent call last):
File "/home/ggreif/miniconda3/envs/snakemake/bin/higlass-manage", line 8, in
sys.exit(cli())
^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ggreif/miniconda3/envs/snakemake/lib/python3.12/site-packages/higlass_manage/view.py", line 157, in view
from higlass.client import Track, View, ViewConf
ModuleNotFoundError: No module named 'higlass.client'

[Thepupa7]

I have the same problem ModuleNotFoundError: No module named 'higlass.client' when i use higlass-manage view .cool. Did you solve it?😭