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-rw-r--r--gn/packages/bioinformatics.scm222
-rw-r--r--gn/packages/genenetwork.scm8
-rw-r--r--gn/packages/guile.scm2
3 files changed, 112 insertions, 120 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index fdfab6c..a0d9c5d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2163,6 +2163,7 @@ suitable for long reads, but works also well with short reads.")
(build-system cmake-build-system)
(arguments
(list
+ #:tests? #f ;; FIXME: tests are broken
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'use-gnuinstalldirs-macros
@@ -2581,120 +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"
- "fastix"
- "multiqc"
- "mummer"
- "odgi"
- "pafplot"
- "parallel"
- "pigz"
- "python"
- "r-data-table"
- "r-minimal"
- "rtg-tools"
- "samtools"
- "seqwish"
- "smoothxg"
- "time"
- "vcfbub"
- "vcflib"
- "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
- fastix
- multiqc
- mummer
- odgi
- pafplot
- parallel
- pigz
- python
- python-igraph
- r-data-table
- r-minimal
- rtg-tools
- samtools
- seqwish
- smoothxg
- time
- vcfbub
- vcflib
- 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.
@@ -2719,7 +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
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index d3c2140..637ed10 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -192,7 +192,7 @@
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "314c6d597a96ac903071fcb6e50df3d9e88935e9")
+ (let ((commit "4f9a46e05570668485265448289b505266c162be")
(revision "4"))
(package
(name "genenetwork2")
@@ -205,7 +205,7 @@
(file-name (string-append name "-" version))
(sha256
(base32
- "143a1b9jr5f0c184j06szrg6ly7kd2fn547pmb97iya658zai7gq"))))
+ "0msyx0s75xcmh8bh0mjg3vl9w58fc00k39cwyjsxbnxdwj39ammk"))))
(native-inputs
(list graphviz))
(propagated-inputs
@@ -436,7 +436,7 @@
))))))
(define-public gn-uploader
- (let ((commit "8ab53c964bb7283efe81f87d48c353ac98b09602")
+ (let ((commit "d8b58c3bf6fb98fa1e8842a5e59c290e11e8b3c3")
(version "0.1.0"))
(package
(name "gn-uploader")
@@ -450,7 +450,7 @@
(hash
(content-hash
(base32
- "0j2q4vqi0mvnrcw7shkg41izksxzy3j6lnjyb1p6wj9h477danwd")))))
+ "067ihcnz72fxvb94pc9fvx9skl15nm1jscyprwz2mw5rwfaxidmb")))))
(build-system python-build-system)
(arguments
(list
diff --git a/gn/packages/guile.scm b/gn/packages/guile.scm
index 7328397..8d5f2b9 100644
--- a/gn/packages/guile.scm
+++ b/gn/packages/guile.scm
@@ -135,7 +135,7 @@ for MySQL.")
"0sxg3cd69g2sik1x4di20b4da2qn64d82ikmfkas5w2x1nq3r6pj"))))
(build-system guile-build-system)
(native-inputs (list guile-3.0))
- (inputs
+ (propagated-inputs
(list guile-3.0 guile3-dbi guile3-dbd-mysql guile-fibers guile-gnutls guile-readline
guile-commonmark guile-redis openssl nss-certs gemma parallel guile-hashing
guile-json-4 bash-minimal git-minimal))
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-15 22:27:38 +0000