* [bug#62980] gnu: bpp-popgen and bppsuite: Update to 2.4.1.
@ 2023-04-21 0:00 MadalinIonel.Patrascu
2023-04-21 0:03 ` [bug#62980] [PATCH 1/2] gnu: bpp-popgen: " Mădălin Ionel Patrașcu
2023-04-21 12:04 ` bug#62980: gnu: bpp-popgen and " Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: MadalinIonel.Patrascu @ 2023-04-21 0:00 UTC (permalink / raw)
To: 62980
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^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#62980] [PATCH 1/2] gnu: bpp-popgen: Update to 2.4.1.
2023-04-21 0:00 [bug#62980] gnu: bpp-popgen and bppsuite: Update to 2.4.1 MadalinIonel.Patrascu
@ 2023-04-21 0:03 ` Mădălin Ionel Patrașcu
2023-04-21 0:03 ` [bug#62980] [PATCH 2/2] gnu: bppsuite: " Mădălin Ionel Patrașcu
2023-04-21 12:04 ` bug#62980: gnu: bpp-popgen and " Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2023-04-21 0:03 UTC (permalink / raw)
To: 62980; +Cc: rekado
* gnu/packages/bioinformatics.scm (bpp-popgen): 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.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
gnu/packages/bioinformatics.scm | 49 +++++++++++++++------------------
1 file changed, 22 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c4cea24632..3969e205b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2296,35 +2296,30 @@ (define-public bpp-phyl-omics
(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.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
- (package
- (name "bpp-popgen")
- (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-popgen")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ population genetics library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-popgen")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-popgen")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
+ (synopsis "Bio++ population genetics library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides population genetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-seq
(package
base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01
prerequisite-patch-id: 5853dbe5778b2160c2bf5dca3f01be75fcbb678c
prerequisite-patch-id: 4af2ed7c595ec571d717d161aff1ef51a8dfc365
prerequisite-patch-id: e460dac992e961a5f13af1ed99bfad48d2f0ceb5
prerequisite-patch-id: 4241e6e34dc593a321a69e135db83293eaf011f7
prerequisite-patch-id: 78c7d0a29aee256ae2df1759863ef7e6dc34102f
prerequisite-patch-id: 4dc46155f0d7730f6996403f20442c2892e08a7c
--
2.39.2
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#62980] [PATCH 2/2] gnu: bppsuite: Update to 2.4.1.
2023-04-21 0:03 ` [bug#62980] [PATCH 1/2] gnu: bpp-popgen: " Mădălin Ionel Patrașcu
@ 2023-04-21 0:03 ` Mădălin Ionel Patrașcu
0 siblings, 0 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2023-04-21 0:03 UTC (permalink / raw)
To: 62980; +Cc: rekado
* gnu/packages/bioinformatics.scm (bppsuite): 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.
[inputs]: Use list.
[home-page]: Changed to github page.
---
gnu/packages/bioinformatics.scm | 56 ++++++++++++++-------------------
1 file changed, 24 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3969e205b3..625dd5a409 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2367,40 +2367,32 @@ (define-public bpp-seq-omics
(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.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
- (package
- (name "bppsuite")
- (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/bppsuite")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (native-inputs
- (list groff man-db texinfo))
- (inputs
- `(("bpp-core" ,bpp-core)
- ("bpp-seq" ,bpp-seq)
- ("bpp-phyl" ,bpp-phyl)
- ("bpp-phyl" ,bpp-popgen)))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bioinformatics tools written with the Bio++ libraries")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bppsuite")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bppsuite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (native-inputs
+ (list groff man-db texinfo))
+ (inputs
+ (list bpp-core bpp-seq bpp-phyl bpp-popgen))
+ (home-page "https://github.com/BioPP")
+ (synopsis "Bioinformatics tools written with the Bio++ libraries")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
package provides command line tools using the Bio++ library.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public blast+
(package
--
2.39.2
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#62980: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
2023-04-21 0:00 [bug#62980] gnu: bpp-popgen and bppsuite: Update to 2.4.1 MadalinIonel.Patrascu
2023-04-21 0:03 ` [bug#62980] [PATCH 1/2] gnu: bpp-popgen: " Mădălin Ionel Patrașcu
@ 2023-04-21 12:04 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2023-04-21 12:04 UTC (permalink / raw)
To: 62980-done
Applied, thank you!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
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2023-04-21 0:00 [bug#62980] gnu: bpp-popgen and bppsuite: Update to 2.4.1 MadalinIonel.Patrascu
2023-04-21 0:03 ` [bug#62980] [PATCH 1/2] gnu: bpp-popgen: " Mădălin Ionel Patrașcu
2023-04-21 0:03 ` [bug#62980] [PATCH 2/2] gnu: bppsuite: " Mădălin Ionel Patrașcu
2023-04-21 12:04 ` bug#62980: gnu: bpp-popgen and " Ricardo Wurmus
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