Some issues I wasn't able to fix

[ericloud]

Hi pachterlab team,

Thanks to have offer us a public access to this pipeline. I try to run it, from scratch and I encounter some issues. I send you a pull request, where I propose some modification to fix some of them. But there's some left where I need your help.

• A missing files in software directory (versions.Rmd), which create this error message:

Error message:
rule get_versions:
output: versions.html
jobid: 7

OMP_NUM_THREADS=1 Rscript --vanilla --default-packages=methods,stats,utils,knitr -e 'setwd(".")' -e 'rmarkdown::render("versions.Rmd", output_file = "versions.html")'
Error in tools::file_path_as_absolute(input) : 
  file 'versions.Rmd' does not exist
Calls: <Anonymous> -> setwd -> dirname -> <Anonymous>
In addition: Warning message:
In normalizePath(path, winslash = winslash, mustWork = mustWork) :
  path[1]="versions.Rmd": No such file or directory
Execution halted
Error in rule get_versions:
    jobid: 7
    output: versions.html

• A missing object or varables, in cufflinks directory on rule investigating_variance, which create this error message:

Quitting from lines 195-203 (investigating_variance.Rmd) 
Error in is.data.table(data) : object 'normalized_counts' not found
Calls: <Anonymous> ... withVisible -> eval -> eval -> melt -> is.data.table

• In geuvadis directory, I have this error message

FileNotFoundError in line 83 of /u/eaudemard/project/kt_paper/sleuth_paper_analysis/geuvadis/Snakefile:
[Errno 2] No such file or directory: 'finn_samples.txt'
  File "/sleuth_paper_analysis/geuvadis/Snakefile", line 83, in <module>

I try generate this file from your resampling_fdr.R script but he need 3 other RData file:

1. ../results/fin_females.RData -> I don't find the way to create it

2. ../results/prep_fin.RData -> that we could create with mean_disp_pairs.R or prep_finnish_samples rule in the snakemake. But this ask to have access to ../results/fin_females.RData

3. ../metadata/geu_meta.RData -> that we can create from metada.R script or with geuvadis_metadata rule in the snakemake

I hope these issues don't come from my side, and that someone can help me, Eric.

[ericloud]

I find ../results/fin_females.RData in the bioRxiv branch. But it's steal missing fastq files, to create finn_samples.txt.

I try to fix it, but I'm steal interested by an answer, Hop-o'-My-Thumb (Little Poucet)