sed issue in OSX, but easily fixable

[alexandruioanvoda]

There is an issue while running GenAPI on Macbooks: the sed in OSX isn't a GNU sed, and because of different params (see example error bellow:), it stops running the analysis.

(base) KIR-Alex-Voda:GFF avoda$ ./genapi
Warning: The following lines have no ID and will be excluded from the analysis:
NODE_3 minced:0.2.0 repeat_region 7508 7779 5 . . note=CRISPR with 5 repeat units;rpt_family=CRISPR;rpt_type=direct
sed: 1: "./017217_ECOR_01_temp.tsv": invalid command code .

A quick fix to that is present here:
https://gist.github.com/andre3k1/e3a1a7133fded5de5a9ee99c87c6fa0d#gistcomment-3082272

Just brew install gnu-sed then add PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" to your ~/.bash_profile, then restart the terminal.