Open iwilkie opened 4 months ago
genome_updater was not tested in mac environments and I don't have one to try it out. However, this seems like a normal script error and can be skipped removing the u
from:
An exemplary trace would be something like
Tools like sed
and cut
behave differently on macOS/OpenBSD.
So the unbound variable
probably means that there is no return value from count_lines_file
.
A possible workaround (untested) would be to use homebrew and install the GNU version of some tools:
brew install coreutils grep findutils gnu-sed
Because brew will prefix the tools with g
to avoid conflicts (e.g., find
-> gfind
), you can also run
export PATH="$HOMEBREW_PREFIX/opt/coreutils/libexec/gnubin:$PATH"
export PATH="$HOMEBREW_PREFIX/opt/grep/libexec/gnubin:$PATH"
export PATH="$HOMEBREW_PREFIX/opt/findutils/libexec/gnubin:$PATH"
export PATH="$HOMEBREW_PREFIX/opt/gnu-sed/libexec/gnubin:$PATH"
in the shell you are going to use genome_updater.
Hi,
I'm trying to run genome updater on a mac (macOS Monterey v12.6.3), I've run into some issues which were previously described and ran the troubleshooting steps (e.g. installing xargs and coreutils). I thought I got it running, but I ran into an issue that I haven't found described before:
This is the line which is throwing the error:
No files were downloaded, and the log doesn't provide more details:
I'm wondering if this issue stems from me working from a mac. Have you encountered this issue before? If yes, is there any workaround or is it not possible because I'm trying to run from a mac?
Thanks, Isa