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ttgump / scDeepCluster

scDeepCluster for Single Cell RNA-seq data
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scDeepCluster in HPC #7

Closed Shicheng-Guo closed 3 years ago

Shicheng-Guo commented 3 years ago

Hi Tiantain,

Is scDeepCluster available for HPC for example SDSC or TACC?

Thanks.

Shicheng

ttgump commented 3 years ago

Hi Tiantain,

Is scDeepCluster available for HPC for example SDSC or TACC?

Thanks.

Shicheng

I am not sure I understand the question correctly, but you can install the dependent packages by conda or pip and then download the source code of scDeepCluster in the HPCs. Are you asking if scDeepCluster available in a package that can be used for HPC by immediate downloading? Best, Tian

Shicheng-Guo commented 3 years ago

Hi Tian, I am wondering which computer system/environment is suggested to run scDeepCluster? AWS? Thanks. Shicheng

ttgump commented 3 years ago

Hi Shicheng, I didn't use AWS but ran experiments on XSEDE comet and expanse. I think they use CentOS Linux 8 and I install the packages by miniconda. The packages are tensorflow 1, Keras and scanpy, and follow the versions I list in the readme file. I found the documents for old Keras here: https://faroit.com/keras-docs/2.1.4/#installation. If you use the new version of scanpy, modify the code "import scanpy.api as sc" to "import scanpy as sc", since new version changed their API name. Let me know if there is any question. Thanks. Best, Tian

Shicheng-Guo commented 3 years ago

Great. Thanks Tian. These information are quite helpful!! Shicheng