gagneurlab / fraser-2.0-analysis Goto Github PK

Dear developer

Thanks for your help in setting up Absplice environment.

I want to try FRASER2.0, but can not install.

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BiocManager::install("c-mertes/FRASER", ref="fraser2")
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing github package(s) 'c-mertes/FRASER'
Downloading GitHub repo c-mertes/FRASER@fraser2
エラー: Failed to install 'FRASER' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.
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FRASER has been successfully installed.

Best regards

Hi Developer!

I add "options(buildtools.check = function(action) TRUE)" so that I successed install

However, snakemake does not work. I was told that I don't have the required data set.

Maybe, I think "snakemake -n Paper_figures/all_figures_R" ? , but this also gave the same error.

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error message

FileNotFoundError in file /var/folders/7d/rr7nqs8x1wq5rv74p18z5ctr0000gn/T/tmp_w5d0ky_, line 575:
[Errno 2] No such file or directory: '/path/to/data/storage/fraser/fraser2/mito/processed_data/variants/prokisch_dna_ids.txt'
File "/Users/idrc/Desktop/FRASER-2.0-analysis-main/Snakefile", line 6, in
File "/Users/idrc/anaconda3/lib/python3.10/site-packages/wbuild/wBuild.snakefile", line 10, in
File "/var/folders/7d/rr7nqs8x1wq5rv74p18z5ctr0000gn/T/tmp_w5d0ky_", line 575, in
##############################################################################################

best regards