From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <62978@debbugs.gnu.org>
Subject: [bug#62978] [PATCH v2 6/6] gnu: Add maffilter.
Date: Fri, 21 Apr 2023 10:16:41 +0200 [thread overview]
Message-ID: <20230421081641.18388-6-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (maffilter): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 511431fb95..169ae39552 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6046,6 +6046,41 @@ (define-public macs
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public maffilter
+ (package
+ (name "maffilter")
+ (version "1.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/jydu/maffilter/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0xgbadjad54hjdh743qszyv4yvdpi45519h6cj6sfgybsr93385l"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; No tests provided.
+ (inputs
+ (list bpp-core
+ bpp-phyl
+ bpp-phyl-omics
+ bpp-seq
+ bpp-seq-omics
+ boost
+ zlib))
+ (home-page "https://jydu.github.io/maffilter/")
+ (synopsis "Multiple alignment format file processor")
+ (description
+ "MafFilter is a program dedicated to the analysis of genome alignments. It
+parses and manipulates @acronym{MAF, multiple alignment format} files as well as
+more simple fasta files. This package can be used to design a pipeline as a
+series of consecutive filters, each performing a dedicated analysis. Many of
+the filters are available, from alignment cleaning to phylogeny reconstruction
+and population genetics analysis. Despite various filtering options and format
+conversion tools, MafFilter can compute a wide range of statistics (phylogenetic
+trees, nucleotide diversity, inferrence of selection, etc.).")
+ (license license:gpl3)))
+
(define-public mafft
(package
(name "mafft")
--
2.39.2
next prev parent reply other threads:[~2023-04-21 10:06 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-04-20 23:02 [bug#62978] gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter MadalinIonel.Patrascu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu
2023-04-21 8:16 ` [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1 Mădălin Ionel Patrașcu
2023-04-21 8:16 ` [bug#62978] [PATCH v2 2/6] gnu: bpp-seq: " Mădălin Ionel Patrașcu
2023-04-21 8:16 ` [bug#62978] [PATCH v2 3/6] gnu: bpp-phyl: " Mădălin Ionel Patrașcu
2023-04-21 8:16 ` [bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics Mădălin Ionel Patrașcu
2023-04-21 8:16 ` [bug#62978] [PATCH v2 5/6] gnu: Add bpp-phyl-omics Mădălin Ionel Patrașcu
2023-04-21 8:16 ` Mădălin Ionel Patrașcu [this message]
2023-04-21 11:16 ` bug#62978: gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter Ricardo Wurmus
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