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wzthu / enrichTF

Bioconductor package enrichTF: Transcription Factors Enrichment Analysis
https://www.bioconductor.org/packages/release/bioc/html/enrichTF.html
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error configuring motifpwm #11

Open justin-malin opened 3 years ago

justin-malin commented 3 years ago

Hi, I am working my way through the vignette and encountered the following error:

PECA_TF_enrich(inputForegroundBed = '/Users/malinjl/Desktop/ATAC-Seq_data/test.bed', genome = "mm10") Configure bsgenome ... Configure bsgenome finished Configure motifpwm ... trying URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz' Error in download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, : cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz' In addition: Warning message: In download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, : cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz': HTTP status was '404 Not Found'

Could you please provide a workaround for this error?

Thanks, Justin

inuritdino commented 3 years ago

I could confirm the same issue. Similarly for mm9 genome.

PECA_TF_enrich(inputForegroundBed = <some_bed_file.bed>, genome = "mm10")

Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
trying URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz'
Error in download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath,  :
  cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz'
In addition: Warning message:
In download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath,  :
  cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz': HTTP status was '404 Not Found'

https://wzthu.github.io/ resource does not seem to exist (well, does not have a web-server up, which for github.io seems to be equal to non-existing). Even more, the repo for the web-link does not have mm9/mm10 genomes, only hg19 and testgenome. Look here: https://github.com/wzthu/wzthu.github.io/tree/master/enrich/refdata

with best.