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 [email protected] wrote:

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

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[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'