gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter.

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3 participants
  • MadalinIonel.Patrascu@mdc-berlin.de
  • Mădălin Ionel Patrașcu
  • Ricardo Wurmus
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unassigned
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MadalinIonel.Patrascu@mdc-berlin.de
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MadalinIonel.Patrascu@mdc-berlin.de wrote 2 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
35e32a70b3e1436081ae3caf98c11582@mdc-berlin.de

Attachment: file
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-3-madalinionel.patrascu@mdc-berlin.de
Date: Thu, 20 Apr 2023 23:59:42 +0200
Subject: [PATCH 3/6] gnu: bpp-phyl: Update to 2.4.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 49 ++++++++++++++-------------------
1 file changed, 20 insertions(+), 29 deletions(-)

Toggle diff (64 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 232d0e42c6..ad61b979dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2244,37 +2244,28 @@ (define-public bpp-core
(license license:cecill-c)))
(define-public bpp-phyl
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
- (package
- (name "bpp-phyl")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ phylogenetic Library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-phyl")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
+ (synopsis "Bio++ phylogenetic library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides phylogenetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-popgen
;; The last release was in 2014 and the recommended way to install from source
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-2-madalinionel.patrascu@mdc-berlin.de
Date: Thu, 20 Apr 2023 23:48:04 +0200
Subject: [PATCH 2/6] gnu: bpp-seq: Update to 2.4.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++--------------------
1 file changed, 19 insertions(+), 29 deletions(-)

Toggle diff (63 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 351387fb06..232d0e42c6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2308,37 +2308,27 @@ (define-public bpp-popgen
(license license:cecill-c))))
(define-public bpp-seq
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
- (package
- (name "bpp-seq")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-seq")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ sequence library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-seq")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/")
+ (synopsis "Bio++ sequence library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides sequence-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bppsuite
;; The last release was in 2014 and the recommended way to install from source
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de
Date: Thu, 20 Apr 2023 23:30:44 +0200
Subject: [PATCH 1/6] gnu: bpp-core: Update to 2.4.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
stored sources.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 42 ++++++++++++++-------------------
1 file changed, 18 insertions(+), 24 deletions(-)

Toggle diff (61 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b27e12a5b4..351387fb06 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2220,34 +2220,28 @@ (define-public qtltools
(license license:gpl3+)))
(define-public bpp-core
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
- (package
- (name "bpp-core")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-core")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "C++ libraries for Bioinformatics")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-core")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"))))
+ (build-system cmake-build-system)
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html")
+ (synopsis "C++ libraries for Bioinformatics")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-phyl
;; The last release was in 2014 and the recommended way to install from source

base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-4-madalinionel.patrascu@mdc-berlin.de
Date: Fri, 21 Apr 2023 00:28:46 +0200
Subject: [PATCH 4/6] gnu: Add bpp-seq-omics.

* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
---
gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad61b979dd..576af31ae6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2321,6 +2321,28 @@ (define-public bpp-seq
library provides sequence-related modules.")
(license license:cecill-c)))
+(define-public bpp-seq-omics
+ (package
+ (name "bpp-seq-omics")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://github.com/BioPP/bpp-seq-omics")
+ (synopsis "Bio++ sequence library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ sequence library.
+It is part of the Bio++ project.")
+ (license license:cecill)))
+
(define-public bppsuite
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-5-madalinionel.patrascu@mdc-berlin.de
Date: Fri, 21 Apr 2023 00:33:13 +0200
Subject: [PATCH 5/6] gnu: Add bpp-phyl-omics.

* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)

Toggle diff (41 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 576af31ae6..93082d8814 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2267,6 +2267,34 @@ (define-public bpp-phyl
library provides phylogenetics-related modules.")
(license license:cecill-c)))
+(define-public bpp-phyl-omics
+ (package
+ (name "bpp-phyl-omics")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ;; I need to check this
+ (inputs
+ (list bpp-core
+ bpp-phyl
+ bpp-seq
+ bpp-seq-omics))
+ (home-page "https://github.com/BioPP/bpp-phyl-omics")
+ (synopsis "Bio++ phylogenetic library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ phylogenetics
+library. It is part of the Bio++ project.")
+ (license license:cecill)))
+
(define-public bpp-popgen
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
(address . 62978@debbugs.gnu.org)
20230420230523.6648-6-madalinionel.patrascu@mdc-berlin.de
Date: Fri, 21 Apr 2023 00:44:40 +0200
Subject: [PATCH 6/6] gnu: Add maffilter.

* gnu/packages/bioinformatics.scm (maffilter): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)

Toggle diff (48 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 93082d8814..c4cea24632 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
MadalinIonel.Patrascu@mdc-berlin.de wrote 2 years ago
(name . control@debbugs.gnu.org)(address . control@debbugs.gnu.org)
641438e8ad6e43ce85e505f242959209@mdc-berlin.de
block 62980 by 62978
Attachment: file
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 3/6] gnu: bpp-phyl: Update to 2.4.1.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
[synopsis]: Use proper capitalization.
---
gnu/packages/bioinformatics.scm | 49 ++++++++++++++-------------------
1 file changed, 20 insertions(+), 29 deletions(-)

Toggle diff (64 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 232d0e42c6..ad61b979dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2244,37 +2244,28 @@ (define-public bpp-core
(license license:cecill-c)))
(define-public bpp-phyl
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
- (package
- (name "bpp-phyl")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ phylogenetic Library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-phyl")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
+ (synopsis "Bio++ phylogenetic library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides phylogenetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-popgen
;; The last release was in 2014 and the recommended way to install from source
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 2/6] gnu: bpp-seq: Update to 2.4.1.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++--------------------
1 file changed, 19 insertions(+), 29 deletions(-)

Toggle diff (63 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 351387fb06..232d0e42c6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2308,37 +2308,27 @@ (define-public bpp-popgen
(license license:cecill-c))))
(define-public bpp-seq
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
- (package
- (name "bpp-seq")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-seq")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ sequence library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-seq")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/")
+ (synopsis "Bio++ sequence library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides sequence-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bppsuite
;; The last release was in 2014 and the recommended way to install from source
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 4/6] gnu: Add bpp-seq-omics.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-4-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
---
gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad61b979dd..576af31ae6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2321,6 +2321,28 @@ (define-public bpp-seq
library provides sequence-related modules.")
(license license:cecill-c)))
+(define-public bpp-seq-omics
+ (package
+ (name "bpp-seq-omics")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://github.com/BioPP/bpp-seq-omics")
+ (synopsis "Bio++ sequence library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ sequence library.
+It is part of the Bio++ project.")
+ (license license:cecill)))
+
(define-public bppsuite
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
stored sources.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 42 ++++++++++++++-------------------
1 file changed, 18 insertions(+), 24 deletions(-)

Toggle diff (61 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b27e12a5b4..351387fb06 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2220,34 +2220,28 @@ (define-public qtltools
(license license:gpl3+)))
(define-public bpp-core
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
- (package
- (name "bpp-core")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-core")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "C++ libraries for Bioinformatics")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-core")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"))))
+ (build-system cmake-build-system)
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html")
+ (synopsis "C++ libraries for Bioinformatics")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-phyl
;; The last release was in 2014 and the recommended way to install from source

base-commit: 904b77e1814b611c256ecf161aa36f58d0882380
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 5/6] gnu: Add bpp-phyl-omics.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-5-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)

Toggle diff (41 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 576af31ae6..511431fb95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2267,6 +2267,34 @@ (define-public bpp-phyl
library provides phylogenetics-related modules.")
(license license:cecill-c)))
+(define-public bpp-phyl-omics
+ (package
+ (name "bpp-phyl-omics")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; No test provided.
+ (inputs
+ (list bpp-core
+ bpp-phyl
+ bpp-seq
+ bpp-seq-omics))
+ (home-page "https://github.com/BioPP/bpp-phyl-omics")
+ (synopsis "Bio++ phylogenetic library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ phylogenetics
+library. It is part of the Bio++ project.")
+ (license license:cecill)))
+
(define-public bpp-popgen
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 6/6] gnu: Add maffilter.
(address . 62978@debbugs.gnu.org)
20230421081641.18388-6-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (maffilter): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)

Toggle diff (48 lines)
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
Ricardo Wurmus wrote 2 years ago
gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter.
(address . 62978-done@debbugs.gnu.org)
87cz3xpjpv.fsf@elephly.net
Thank you for these patches. I applied them.

maffilter needed some changes:

- formatting
- license
- git-fetch vs url-fetch (can’t use generated archive URLs)
- sorting of inputs

--
Ricardo
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