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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
MIT License
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Installation of Baysor from Julia #123

Closed sdwien closed 1 month ago

sdwien commented 1 month ago

Dear Baysor Team,

I am following the installation instructions from 10x Genomics for Xenium data here (working on Ubuntu 20):

https://www.10xgenomics.com/analysis-guides/using-baysor-to-perform-xenium-cell-segmentation

I installed Julia version 1.8.5 . I downloaded Baysor from here: curl -L -O https://github.com/kharchenkolab/Baysor/archive/refs/heads/master.zip

After the Julia code for package compilation:

using Pkg
Pkg.add(Pkg.PackageSpec(;name="PackageCompiler"))
Pkg.activate(".")
Pkg.instantiate()

however, I do not have a new subdirectory Baysor-master/bin , so the next suggested step ( julia julia ./bin/build.jl ) cannot be run.

Is there one step or more missing in the workflow on the 10x Genomics page? Many thanks for your suggestions and help, best regards, Sophia

sdwien commented 1 month ago

Update: I tried alternatively to install using julia as described in the Baysor manual, and the following command worked for me: julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.build()' Thanks, will close this issue now. Best, Sophia