From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 38505@debbugs.gnu.org,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#38505] [PATCH] gnu: Add fast-screen.
Date: Fri, 18 Mar 2022 00:13:37 -0400 [thread overview]
Message-ID: <87o8236gpa.fsf_-_@gmail.com> (raw)
In-Reply-To: <87immfc2qc.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 16 Dec 2019 23:41:47 +0100")
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
prev parent reply other threads:[~2022-03-18 4:14 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2019-12-05 21:21 [bug#38505] [PATCH] gnu: Add fast-screen Mădălin Ionel Patrașcu
2019-12-11 2:16 ` Efraim Flashner
2019-12-16 22:41 ` Ricardo Wurmus
2022-03-18 4:13 ` Maxim Cournoyer [this message]
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