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[bug#38505] [PATCH] gnu: Add fast-screen.
From: |
Maxim Cournoyer |
Subject: |
[bug#38505] [PATCH] gnu: Add fast-screen. |
Date: |
Fri, 18 Mar 2022 00:13:37 -0400 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) |
Hello,
Ricardo Wurmus <rekado@elephly.net> writes:
> 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!
Some 2 years later, are you still up to the challenge hinted at by
Ricardo? :-)
Thanks,
Maxim
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