Mark Ziemann

Dat sync errror

1

I am reporting: - [x ] a bug or unexpected behavior - [x] general feedback - [ ] feature request - [ ] security issue # Bug Report Please give...

I am reporting: - [x ] a bug or unexpected behavior - [ ] general feedback - [ ] feature request - [ ] security issue # Bug Report Please...

After fixing the typo, it passed devtools::check() (I'm hoping to see this package in CRAN some time as its dependancy for a pkg I'm working on)

Pysradb to fetch SRA metadata?

2

This looks like a more stable alternative https://github.com/saketkc/pysradb

Time to include some extra species

6

6th FEB 2020 | no. SRX -- | -- Arabidopsis thaliana | 30890 Zea mays | 19753 Oryza sativa | 9737 Triticum aestivum | 6924 Solanum lycopersicum | 6444 Sorghum...

Download automatically times out after 60 seconds

1

https://github.com/satijalab/seurat-data/blob/d6a8ce61ccb21a3b204f194d07009772c822791d/R/seurat_data.R#L82C1-L82C20 My `InstallData("ifnb") ` command was terminated after downloading 341 of 390MB as it his the 60 seconds timeout limit. This default timeout is okay for small files

So there is a known issue where this happens https://github.com/relipmoc/skewer/issues/24 (Perhaps unsuprisingly... from Torsten!) Solution is to run with -f sanger. skewer -f sanger SRR6747861_1.fastq SRR6747861_2.fastq