GNU bug report logs - #38505
[PATCH] gnu: Add fast-screen.

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Package: guix-patches; Reported by: Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>; Keywords: moreinfo patch; dated Thu, 5 Dec 2019 21:22:01 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
To: Ricardo Wurmus <rekado@HIDDEN>
Subject: Re: bug#38505: [PATCH] gnu: Add fast-screen.
References: <20191205212114.4971-1-madalinionel.patrascu@HIDDEN>
 <87immfc2qc.fsf@HIDDEN>
Date: Fri, 18 Mar 2022 00:13:37 -0400
In-Reply-To: <87immfc2qc.fsf@HIDDEN> (Ricardo Wurmus's message of "Mon,
 16 Dec 2019 23:41:47 +0100")
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Hello,

Ricardo Wurmus <rekado@HIDDEN> writes:

> Hi M=C4=83d=C4=83lin,
>
>> * gnu/packages/bioinformatics.scm (fast-screen): New variable.
>
> I don=E2=80=99t 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=E2=80=99s PATH, such as Bismark (which is writte=
n 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=E2=80=99t yield a usable tool =
I=E2=80=99m
> 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=E2=80=99t count on upstream to change this and pat=
ch the
> source file by ourselves.  One way is to patch every invocation of an
> external command; another is to wrap the script itself (with
> =E2=80=9Cwrap-script=E2=80=9D) in PATH and PERL5PATH to provide a suitabl=
e 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
Information forwarded to guix-patches@HIDDEN:
bug#38505; Package guix-patches. Full text available.
Added tag(s) moreinfo. Request was from Maxim Cournoyer <maxim.cournoyer@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

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 <madalinionel.patrascu@HIDDEN>
Subject: Re: [bug#38505] [PATCH] gnu: Add fast-screen.
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Hi M=C4=83d=C4=83lin,

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

I don=E2=80=99t 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=E2=80=99s 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=E2=80=99t yield a usable tool I=
=E2=80=99m
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=E2=80=99t 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
=E2=80=9Cwrap-script=E2=80=9D) 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
Information forwarded to guix-patches@HIDDEN:
bug#38505; Package guix-patches. Full text available.

Message received at 38505 <at> debbugs.gnu.org:


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Subject: Re: [bug#38505] [PATCH] gnu: Add fast-screen.
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It's not clear to me what perl is used for in this package.

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Information forwarded to guix-patches@HIDDEN:
bug#38505; Package guix-patches. Full text available.

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To: <guix-patches@HIDDEN>
Subject: [PATCH] gnu: Add fast-screen.
Date: Thu, 5 Dec 2019 22:21:14 +0100
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* gnu/packages/bioinformatics.scm (fast-screen): New variable.
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74a44874ee..53e4c7296f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15341,3 +15341,56 @@ methylation metrics from them.  MethylDackel requires an indexed fasta file
 containing the reference genome as well.")
     ;; See https://github.com/dpryan79/MethylDackel/issues/85
     (license license:expat)))
+
+(define-public fastq-screen
+  (package
+    (name "fastq-screen")
+    (version "0.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.bioinformatics.babraham.ac.uk/projects/"
+			   "fastq_screen/fastq_screen_v" version ".tar.gz"))
+       (sha256
+        (base32
+         "0m7n9b1pr8rk1pd3va0mr69pd7gddcsvrvlk2s7907i02wkc1say"))))
+    (build-system trivial-build-system)
+    (arguments
+     ;; it is just an extraction processs
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+	 (use-modules (guix build utils))
+	 (let* ((tar (assoc-ref %build-inputs "tar"))
+	        (gzip (assoc-ref %build-inputs "gzip"))
+	        (out (assoc-ref %outputs "out"))
+	        (doc (string-append out "/share/doc"))
+	        (bin (string-append out "/bin")))
+	   (setenv "PATH" (string-append tar "/bin:" gzip "/bin"))
+	   (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+	   (chdir (string-append "fastq_screen_v" ,version))
+           (install-file "fastq_screen" bin)
+	   (install-file "fastq_screen.conf.example" doc)
+	   (install-file "fastq_screen_documentation.md" doc)
+	   (install-file "RELEASE_NOTES.txt" doc)
+	   #t))))
+    (inputs
+     `(("perl" ,perl)))
+    (native-inputs
+     `(("gzip" ,gzip)
+       ("tar" ,tar)))
+    (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/")
+    (synopsis "FastQ Screen allows to search a large sequence dataset")
+    (description
+     "FastQ Screen is an application which allows you to search a large sequence
+dataset against a panel of different databases to build up a picture of where
+the sequences in your data originate.  The program was built as a quality
+control check for sequencing pipelines but may also have uses in metagenomics
+studies where mixed samples are expected.  The application generates both text
+and graphical output to inform you what proportion of your library was able to
+map, either uniquely or to more than one location, against each of your
+specified reference genomes.  The user should therefore be able to identify a
+clean sequencing experiment in which the overwhelming majority of reads are
+probably derived from a single genomic origin.")
+    (license license:gpl3+)))
+
-- 
2.17.1
Acknowledgement sent to Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.
Report forwarded to guix-patches@HIDDEN:
bug#38505; Package guix-patches. Full text available.
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