* [bug#62978] gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. @ 2023-04-20 23:02 MadalinIonel.Patrascu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (2 more replies) 0 siblings, 3 replies; 14+ messages in thread From: MadalinIonel.Patrascu @ 2023-04-20 23:02 UTC (permalink / raw) To: 62978 [-- Attachment #1: Type: text/plain, Size: 2 bytes --] [-- Attachment #2: Type: text/html, Size: 830 bytes --] ^ permalink raw reply [flat|nested] 14+ messages in thread
* [bug#62978] 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 ` Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (4 more replies) 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 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 2 siblings, 5 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu @ 2023-04-20 23:05 ` Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (3 subsequent siblings) 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] 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 ` Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (2 subsequent siblings) 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] 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 ` Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (2 preceding siblings ...) 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu @ 2023-04-20 23:05 ` Mădălin Ionel Patrașcu 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu ` (3 preceding siblings ...) 2023-04-20 23:05 ` [bug#62978] Mădălin Ionel Patrașcu @ 2023-04-20 23:05 ` Mădălin Ionel Patrașcu 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-20 23:05 UTC (permalink / raw) To: 62978 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1. 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 @ 2023-04-21 8:16 ` Mădălin Ionel Patrașcu 2023-04-21 8:16 ` [bug#62978] [PATCH v2 2/6] gnu: bpp-seq: " Mădălin Ionel Patrașcu ` (4 more replies) 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 2 siblings, 5 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 2/6] gnu: bpp-seq: Update to 2.4.1. 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 ` Mădălin Ionel Patrașcu 2023-04-21 8:16 ` [bug#62978] [PATCH v2 3/6] gnu: bpp-phyl: " Mădălin Ionel Patrașcu ` (3 subsequent siblings) 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 3/6] gnu: bpp-phyl: Update to 2.4.1. 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 ` Mădălin Ionel Patrașcu 2023-04-21 8:16 ` [bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics Mădălin Ionel Patrașcu ` (2 subsequent siblings) 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics. 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 ` 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 ` [bug#62978] [PATCH v2 6/6] gnu: Add maffilter Mădălin Ionel Patrașcu 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 5/6] gnu: Add bpp-phyl-omics. 2023-04-21 8:16 ` [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1 Mădălin Ionel Patrașcu ` (2 preceding siblings ...) 2023-04-21 8:16 ` [bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics Mădălin Ionel Patrașcu @ 2023-04-21 8:16 ` Mădălin Ionel Patrașcu 2023-04-21 8:16 ` [bug#62978] [PATCH v2 6/6] gnu: Add maffilter Mădălin Ionel Patrașcu 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* [bug#62978] [PATCH v2 6/6] gnu: Add maffilter. 2023-04-21 8:16 ` [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1 Mădălin Ionel Patrașcu ` (3 preceding siblings ...) 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 4 siblings, 0 replies; 14+ messages in thread From: Mădălin Ionel Patrașcu @ 2023-04-21 8:16 UTC (permalink / raw) To: 62978 * 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 ^ permalink raw reply related [flat|nested] 14+ messages in thread
* bug#62978: gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. 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 2023-04-21 8:16 ` [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1 Mădălin Ionel Patrașcu @ 2023-04-21 11:16 ` Ricardo Wurmus 2 siblings, 0 replies; 14+ messages in thread From: Ricardo Wurmus @ 2023-04-21 11:16 UTC (permalink / raw) To: 62978-done 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 ^ permalink raw reply [flat|nested] 14+ messages in thread
end of thread, other threads:[~2023-04-21 11:19 UTC | newest] Thread overview: 14+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 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 ` [bug#62978] [PATCH v2 6/6] gnu: Add maffilter Mădălin Ionel Patrașcu 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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