When running multiple_join_paired_ends.py I encountered the error:
Cannot find fastq-join. Is it installed? Is it in your path?
The solution was apparently to install ea-utils, which contains fastq-join.
So I tried that.
However, make failed with the same error as detailed here: https://groups.google.com/forum/#!msg/ea-utils/nR5qvhgZKIY/yx5BSEta_dQJ
The trick here was that not everything in ea-utils was required to make fastq-join work, as Eric Aronesty pointed out on the above thread:
“Of course fastq-join doesn’t use sparse-hash… so if you ran “make fastq-join” … it would work, even on a Mac.”
Then of course you need to move the resulting fastq-join binary to somewhere in your path. Now multiple_join_paired_ends.py should work fine.