Shuffle PDF 2-up in shell
Thanks to @IconDaemon,
the solution is like this:

cpdf -twoup-stack my-file.pdf -o out.pdf
cpdf -rotate 90 out.pdf -o out2.pdf
cpdf -scale-to-fit "210mm 297mm" out2.pdf -o my-file-collated.pdf
rm out.pdf out2.pdf