[bug#62978] gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter.

[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]

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[bug#62978]

[Mădălin Ionel Patrașcu]

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(-)

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

[bug#62978]

[Mădălin Ionel Patrașcu]

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(-)

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

[bug#62978]

[Mădălin Ionel Patrașcu]

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(-)

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

[bug#62978]

[Mădălin Ionel Patrașcu]

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(+)

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

[bug#62978]

[Mădălin Ionel Patrașcu]

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(+)

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

[bug#62978]

[Mădălin Ionel Patrașcu]

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(+)

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

[bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1.

[Mădălin Ionel Patrașcu]

* 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(-)

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

[bug#62978] [PATCH v2 2/6] gnu: bpp-seq: Update to 2.4.1.

[Mădălin Ionel Patrașcu]

* 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(-)

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

[bug#62978] [PATCH v2 3/6] gnu: bpp-phyl: Update to 2.4.1.

[Mădălin Ionel Patrașcu]

* 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(-)

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

[bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics.

[Mădălin Ionel Patrașcu]

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

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

[bug#62978] [PATCH v2 5/6] gnu: Add bpp-phyl-omics.

[Mădălin Ionel Patrașcu]

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

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

[bug#62978] [PATCH v2 6/6] gnu: Add maffilter.

[Mădălin Ionel Patrașcu]

* 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

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]

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