search

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
301 stars 125 forks source link

snaptools: command not found #70

Closed ScienceBear closed 5 years ago

ScienceBear commented 5 years ago

Hi Rongxin,

I've been trying to get SnapATAC up and running, but am struggling to run snaptools. I've tried installing snaptools both by cloning from GitHub and downloading using pip (in ubuntu on a windows system), and installation is apparently successful in both instances.

If I try and uninstall snaptools pip can locate the files (/home/luke/.local/bin/snaptools), installed version is 14.7.

However while trying to complete the 10X Adult Brain Fresh 5K vignette I encounter an error when trying to run snap-pre: I get "snaptools: command not found" returned. I've manually added "/home/luke/.local" to the $PATH in case linux wasn't able to find snaptools, but that's not helped.

I've not extensive experience in Linux so this may be a basic user error, as despite searching google I've not found any accounts of similar problems.

Hope you can advise!

ScienceBear commented 5 years ago

I fixed the issue, it turns out some of the dependencies were incompatible with R v3.4, have managed to update to v3.6.1 using Michael Rutter's PPA.