Subject: Re: [bug#38505] [PATCH] gnu: Add fast-screen.

From: Ricardo Wurmus <[email-masked]>
Date: Mon, 16 Dec 2019 23:41:47 +0100

Hi Mădălin,

> * gnu/packages/bioinformatics.scm (fast-screen): New variable.

I don’t think this package actually produces a usable output.

Frustratingly, this is a Perl script which calls out to tools that
happen to be on the user’s PATH, such as Bismark (which is written in
the same style, so it may be enlightening to read its package
definition), bwa, or bowtie.

Simply copying the script to the store won’t yield a usable tool I’m
afraid.

For Bismark I talked to the authors in the past in the hopes of
simplifying configuration at build time, but they were not interested in
changing the tool to accomodate any other case than the one Bismark was
designed for: to be unpacked in an already suitable environment.

This means that we can’t count on upstream to change this and patch the
source file by ourselves.  One way is to patch every invocation of an
external command; another is to wrap the script itself (with
“wrap-script”) in PATH and PERL5PATH to provide a suitable environment
at runtime.  (Wrapping PERL5PATH may be necessary anyway to ensure that
Perl can find the required modules.)

Good luck!

--
Ricardo