missing files

[conchoecia]

Hello,

I am trying to download some files from your study but it seems like some files are missing from the latest version of the repo. With ./launchme.sh download all I end up with this error: YeastStrainsStudy/utils/src/locpy/bin/activate: No such file or directory.

Alternatively, could you just make a readme that has the accession numbers for each sample? That would be very useful for me.

Thank you!

[fg6]

Hi!
sorry you are having problems. It seems something is wrong with the python installation.
Before trying to download, did you do a:
./launchme.sh install
and if so, did you get any error?

I will try to collect all the accession numbers in one place, but I would appreciate if you help me
understand what is going wrong, so to fix the issue.

Thank you,
Francesca

[conchoecia]

Hi Francesca,

Thanks for your message - I just want to download the raw data itself and am using the bash script because the manuscript and its supplement do not list the URLs or accession numbers for any of the samples. Could you possibly just provide the accession numbers in the README.md since that information is hard to find?

In any case, I spun up a docker image and ran the install script which went OK, but now it seems that the URLs are somewhere else. Here's the log -

root@305c49dcdd82:/data/YeastStrainsStudy# bash launchme.sh install

 Downloading and installing some utilities...

  creating a local python environment...
root@305c49dcdd82:/data/YeastStrainsStudy# ls
README.md  launchme.sh  pipelines  utils
root@305c49dcdd82:/data/YeastStrainsStudy# ./launchme.sh download all

 Downloading and preparing data...


   preparing ONT data for  s288c 1
           downloading data
      !!! Unexpected Error! Could not find url  ftp://ftp.sra.ebi.ac.uk/vol1/ERA846/ERA846167/oxfordnanopore_native/data_Sanger_FAA86705_s288c_5_a_d.tar.gz
root@305c49dcdd82:/data/YeastStrainsStudy#

Thanks!

[conchoecia]

I found the data! :)

I am happy to rerun your pipeline if you would like me to check anything else out!

[fg6]

Hi,
sorry you were still having problems, I am glad you found everything now :).
I checked the url in your printout, and it's still available, not sure why you are having that problem,
maybe some network problem or some firewall limitations?

Anyways, all the data locations are listed in the file: utils/runlist.sh .
As soon as I have a bit of time I will make this a bit more accessible and easy to find,
thanks for your suggestion!

Francesca