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wanglab-broad / ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression
GNU General Public License v3.0
41 stars 11 forks source link

Failed to install #1

Closed lainnorton closed 2 years ago

lainnorton commented 2 years ago

Hi authors,

I tried to use pip install git+https://github.com/LiuLab-Bioelectronics-Harvard/ClusterMap.git to install, but it showed "Command errored out with exit status 128".

I changed "git+https" to "git+git". This time it could be downloaded successfully, but the site-packages folder only contained "ClusterMap-0.0.1.dist-info", which cannot be imported.

I finally tried to use git clone and used the command python setup.py install to install. But it showed "warning: install_lib:'build/lib' does not exist - no Python modules to install".

What should I do to successfully install ClusterMap?

yichunher commented 2 years ago

Hi,

Thanks for asking!

Could you try first git clone https://github.com/wanglab-broad/ClusterMap.git to download the package locally, then cd ClusterMap and pip install -e.?

For the environment, I added a .yml file so you can use conda env create -f environment.yml to create a good environment named ClusterMap with required packages. Thanks!

lainnorton commented 2 years ago

Hi,

Thanks for asking!

Could you try first git clone https://github.com/wanglab-broad/ClusterMap.git to download the package locally, then cd ClusterMap and pip install -e.?

For the environment, I added a .yml file so you can use conda env create -f environment.yml to create a good environment named ClusterMap with required packages. Thanks!

Hi @heihaizhengdong

Thanks for the reply! Through this way, I successfully installed ClusterMap and imported.

Thanks!

rocketeer1998 commented 2 years ago

Hi @heihaizhengdong , I'm installing ClusterMap on my Windows10 computer following your instruction. But I got a long list of ResolvePackageNotFound error after typing conda env create -f environment.yml. I've tried to solve this problem by moving the problematic dependencies from dependencies to pip. So the environment is successfully created. However, I still can't import the modules that i need in Clustermap. Any recommendations?

ruqianl commented 2 years ago

@rocketeer1998 Yeah, I had the same error on Linux. After some digging, I found that the provided yml only works for Mac since it specifies the platform-specific build versions. See: https://stackoverflow.com/questions/55554431/conda-fails-to-create-environment-from-yml/55576493#55576493

Basically, removing the "=hddfnxxx" should fix it.

westalone commented 1 year ago

I am trying to install ClusterMap on HPC(CentOS) using this trick, but the system still failed to install, a lot of conflicting packages....Any clues to solve it? Thanks a lot!

Basically, removing the "=hddfnxxx" should fix it.