GNU bug report logs - #32819
[PATCH] gnu: Add porechop.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Leo Famulari <leo <at> famulari.name>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#32819: closed ([PATCH] gnu: Add porechop.)
Date: Sun, 30 Sep 2018 18:12:02 +0000

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Your message dated Sun, 30 Sep 2018 14:10:57 -0400
with message-id <20180930181057.GA5218 <at> jasmine.lan>
and subject line Re: [bug#32819] [PATCH] gnu: Add porechop.
has caused the debbugs.gnu.org bug report #32819,
regarding [PATCH] gnu: Add porechop.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: ricardo.wurmus <at> mdc-berlin.de, pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add porechop.
Date: Mon, 24 Sep 2018 15:31:14 +0200

* gnu/packages/bioinformatics.scm (porechop): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b619866ba..2ab7135f5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13760,3 +13760,33 @@ sequencing data.")
     ;; This is free software but the license variant is unclear:
     ;; <https://github.com/mw55309/poRe_docs/issues/10>.
     (license license:bsd-3)))
+
+(define-public porechop
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Porechop#installation
+  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
+        (revision "1"))
+    (package
+      (name "porechop")
+      (version (git-version "0.2.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Porechop.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
+      (build-system python-build-system)
+      (home-page "https://github.com/rrwick/porechop")
+      (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
+      (description
+       "The porechop package is a tool for finding and removing adapters from Oxford
+Nanopore reads.  Adapters on the ends of reads are trimmed off, and when a read
+has an adapter in its middle, it is treated as chimeric and chopped into
+separate reads.  Porechop performs thorough alignments to effectively find
+adapters, even at low sequence identity.  Porechop also supports demultiplexing
+of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
+Barcoding Kit or Rapid Barcoding Kit.")
+      (license license:gpl3))))
-- 
2.17.1

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From: Leo Famulari <leo <at> famulari.name>
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 32819-done <at> debbugs.gnu.org, ricardo.wurmus <at> mdc-berlin.de
Subject: Re: [bug#32819] [PATCH] gnu: Add porechop.
Date: Sun, 30 Sep 2018 14:10:57 -0400

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On Mon, Sep 24, 2018 at 03:31:14PM +0200, pimi wrote:
> * gnu/packages/bioinformatics.scm (porechop): New variable.

Thanks!

> +      (license license:gpl3))))

I used gpl3+ and pushed as f2bc53af70eea7b7147b9e7e40280941866ed128

For more information about the license, see here:
<https://github.com/rrwick/Porechop/blob/master/porechop/porechop.py#L8>

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