gn: pggb: Update to 0.7.2.

* gn/packages/bioinformatics.scm (pggb): Update to 0.7.2.

1 files changed, 106 insertions, 107 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2e799ea..a0d9c5d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2582,112 +2582,111 @@ multiple sequence alignment.")
         license:boost1.0)))) ; catch.hpp
 
 (define-public pggb
-  (let ((commit "9ebff27320382e470ed38a85b4448402e1e7c353")
-        (revision "1"))
-    (package
-      (name "pggb")
-      (version (git-version "0.5.1" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/pangenome/pggb")
-                       (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32 "0rgpj52q3ai7f1saqbilgx5gz4f403x3427wq649qwv84ivmi1sf"))))
-      (build-system copy-build-system)
-      (arguments
-       (list
-         #:install-plan
-         #~'(("pggb" "bin/")
-             ("partition-before-pggb" "bin/")
-             ("scripts/" "bin/")
-             ("scripts" "bin/scripts"))
-         #:phases
-         #~(modify-phases %standard-phases
-             (add-after 'unpack 'force-python3
-               (lambda _
-                 (substitute* (find-files "scripts" "\\.py$")
-                   (("/usr/bin/python") "/usr/bin/python3"))))
-             (add-before 'install 'patch-and-wrap-scripts
-               (lambda* (#:key inputs #:allow-other-keys)
-                 (substitute* "scripts/vcf_preprocess.sh"
-                   (("bcftools ")
-                    (string-append (search-input-file inputs "/bin/bcftools") " ")))
-                 (wrap-script "scripts/net2communities.py"
-                   `("GUIX_PYTHONPATH" ":" prefix
-                     (,(getenv "GUIX_PYTHONPATH"))))))
-             (add-after 'install 'wrap-scripts
-               (lambda* (#:key inputs outputs #:allow-other-keys)
-                 (let ((out (assoc-ref outputs "out")))
-                   (for-each
-                     (lambda (file)
-                       (wrap-script file
-                         `("R_LIBS_SITE" ":" prefix
-                           (,(getenv "R_LIBS_SITE")))
-                         `("PATH" ":" prefix
-                           ,(map (lambda (input) (string-append input "/bin"))
-                                 '#$(map (lambda (label)
-                                           (or (this-package-input (string-append label "-hwcaps"))
-                                               (this-package-input label)))
-                                         (list "bc"
-                                               "bcftools"
-                                               "bedtools"
-                                               "gfaffix"
-                                               "htslib"
-                                               "multiqc"
-                                               "odgi"
-                                               "parallel"
-                                               "pigz"
-                                               "python"
-                                               "r-data-table"
-                                               "r-minimal"
-                                               "rtg-tools"
-                                               "samtools"
-                                               "seqwish"
-                                               "smoothxg"
-                                               "time"
-                                               "vcfbub"
-                                               "vg"
-                                               "wfmash"))))))
-                          (list (string-append out "/bin/pggb")
-                                (string-append out "/bin/partition-before-pggb")
-                                (string-append out "/bin/gfa2evaluation.sh")
-                                (string-append out "/bin/scripts/gfa2evaluation.sh"))))))
-             (add-after 'install 'substitute-file-paths
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (let ((out (assoc-ref outputs "out")))
-                   (substitute* (string-append out "/bin/gfa2evaluation.sh")
-                     (("/usr/local/bin/vcf_preprocess.sh")
-                      (string-append out "/bin/vcf_preprocess.sh"))
-                     (("/usr/local/bin/nucmer2vcf.R")
-                      (string-append out "/bin/nucmer2vcf.R")))))))))
-      (inputs
-       (list bc
-             bcftools
-             bedtools
-             gfaffix
-             guile-3.0      ; for wrap-script
-             htslib         ; tabix
-             multiqc
-             odgi
-             parallel
-             pigz
-             python
-             python-igraph
-             r-data-table
-             r-minimal
-             rtg-tools
-             samtools
-             seqwish
-             smoothxg
-             time
-             vcfbub
-             vg
-             wfmash))
-      (home-page "https://doi.org/10.1101/2023.04.05.535718")
-      (synopsis "PanGenome Graph Builder")
-      (description "@command{pggb} builds
+  (package
+    (name "pggb")
+    (version "0.7.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pangenome/pggb")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1k3ffl5h5jqnz9k9y5cjqr8z6hh0gyjfj4szggz11lncp5wkskgv"))))
+    (build-system copy-build-system)
+    (arguments
+     (list
+      #:install-plan
+      #~'(("pggb" "bin/")
+          ("partition-before-pggb" "bin/")
+          ("scripts/" "bin/")
+          ("scripts" "bin/scripts"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'force-python3
+            (lambda _
+              (substitute* (find-files "scripts" "\\.py$")
+                (("/usr/bin/python") "/usr/bin/python3"))))
+          (add-before 'install 'patch-and-wrap-scripts
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "scripts/vcf_preprocess.sh"
+                (("bcftools ")
+                 (string-append (search-input-file inputs "/bin/bcftools") " ")))
+              (wrap-script "scripts/net2communities.py"
+                           `("GUIX_PYTHONPATH" ":" prefix
+                             (,(getenv "GUIX_PYTHONPATH"))))))
+          (add-after 'install 'wrap-scripts
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (for-each
+                 (lambda (file)
+                   (wrap-script file
+                                `("R_LIBS_SITE" ":" prefix
+                                  (,(getenv "R_LIBS_SITE")))
+                                `("PATH" ":" prefix
+                                  ,(map (lambda (input) (string-append input "/bin"))
+                                        '#$(map (lambda (label)
+                                                  (or (this-package-input (string-append label "-hwcaps"))
+                                                      (this-package-input label)))
+                                                (list "bc"
+                                                      "bcftools"
+                                                      "bedtools"
+                                                      "gfaffix"
+                                                      "htslib"
+                                                      "multiqc"
+                                                      "odgi"
+                                                      "parallel"
+                                                      "pigz"
+                                                      "python"
+                                                      "r-data-table"
+                                                      "r-minimal"
+                                                      "rtg-tools"
+                                                      "samtools"
+                                                      "seqwish"
+                                                      "smoothxg"
+                                                      "time"
+                                                      "vcfbub"
+                                                      "vg"
+                                                      "wfmash"))))))
+                 (list (string-append out "/bin/pggb")
+                       (string-append out "/bin/partition-before-pggb")
+                       (string-append out "/bin/gfa2evaluation.sh")
+                       (string-append out "/bin/scripts/gfa2evaluation.sh"))))))
+          (add-after 'install 'substitute-file-paths
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (substitute* (string-append out "/bin/gfa2evaluation.sh")
+                  (("/usr/local/bin/vcf_preprocess.sh")
+                   (string-append out "/bin/vcf_preprocess.sh"))
+                  (("/usr/local/bin/nucmer2vcf.R")
+                   (string-append out "/bin/nucmer2vcf.R")))))))))
+    (inputs
+     (list bc
+           bcftools
+           bedtools
+           gfaffix
+           guile-3.0                    ; for wrap-script
+           htslib                       ; tabix
+           multiqc
+           odgi
+           parallel
+           pigz
+           python
+           python-igraph
+           r-data-table
+           r-minimal
+           rtg-tools
+           samtools
+           seqwish
+           smoothxg
+           time
+           vcfbub
+           vg
+           wfmash))
+    (home-page "https://doi.org/10.1101/2023.04.05.535718")
+    (synopsis "PanGenome Graph Builder")
+    (description "@command{pggb} builds
 @url{https://doi.org/10.1146%2Fannurev-genom-120219-080406, pangenome}
 @url{https://doi.org/10.1038/nbt.4227, variation graphs} from a set of input
 sequences.
@@ -2712,7 +2711,7 @@ such as the @url{https://github.com/vgteam/vg, vg} and
 @command{pggb} has been tested at scale in the @acronym{Human Pangenome
 Reference Consortium, HPRC} as a method to build a graph from the
 @url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define use-glibc-hwcaps
   (package-input-rewriting/spec