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-rw-r--r--gn/packages/bioinformatics.scm273
1 files changed, 157 insertions, 116 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3f89abe..02c979d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -41,6 +41,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages cran)
+ #:use-module (gnu packages crates-compression)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages crates-graphics)
#:use-module (gnu packages curl)
@@ -2163,6 +2164,7 @@ 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
@@ -2580,121 +2582,159 @@ multiple sequence alignment.")
license:zlib ; deps/sonLib/externalTools/cutest
license:boost1.0)))) ; catch.hpp
+(define-public wfmash-0.14
+ (package
+ (inherit wfmash)
+ (version "0.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
+ version "/wfmash-v" version ".tar.gz"))
+ (sha256
+ (base32
+ "1mk3jschn3hdr45glds65g3hxk7v6nc3plkvxmfbd5pr4kyzlf13"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ ;; Unbundle atomic-queue.
+ (delete-file-recursively "src/common/atomic_queue")
+ (substitute* "src/align/include/computeAlignments.hpp"
+ (("\"common/atomic_queue/atomic_queue.h\"")
+ "<atomic_queue/atomic_queue.h>"))
+ ;; Remove compiler optimizations.
+ (substitute* (find-files "." "CMakeLists\\.txt")
+ (("-march=native ") ""))))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments wfmash)
+ ((#:tests? tests? #f) #f)
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (replace 'build-check-prerequisites
+ (lambda _
+ (let ((wfa2-lib #$(string-append "../wfmash-v"
+ version
+ "/src/common/wflign/deps/WFA2-lib")))
+ (substitute* (string-append wfa2-lib "/Makefile")
+ ;; Remove architecture-specific flags.
+ (("-march=x86-64-v3") ""))
+ (substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
+ ;; Fix time command.
+ (("\\\\time -v") "time"))
+ ;; Build wfa2-lib.
+ (invoke "make" "-C" wfa2-lib
+ #$(string-append "CC=" (cc-for-target))))))))))
+ (inputs
+ (modify-inputs (package-inputs wfmash)
+ (prepend jemalloc)
+ (delete "libdeflate")))))
+
(define-public pggb
- (let ((commit "9ebff27320382e470ed38a85b4448402e1e7c353")
- (revision "1"))
- (package
- (name "pggb")
- (version (git-version "0.5.1" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pangenome/pggb")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0rgpj52q3ai7f1saqbilgx5gz4f403x3427wq649qwv84ivmi1sf"))))
- (build-system copy-build-system)
- (arguments
- (list
- #:install-plan
- #~'(("pggb" "bin/")
- ("partition-before-pggb" "bin/")
- ("scripts/" "bin/")
- ("scripts" "bin/scripts"))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'force-python3
- (lambda _
- (substitute* (find-files "scripts" "\\.py$")
- (("/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-0.14))
+ (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 +2759,7 @@ 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
@@ -4445,7 +4485,7 @@ automatically vectorize for different architectures without adapting the code.")
(define-public r-rrbgen
(package
- (name "r-stitch")
+ (name "r-rrbgen")
(version "0.0.6")
(source
(origin
@@ -4554,6 +4594,7 @@ interface to the basic htslib. It can be easily included in a C++
program for scripting high-performance genomic analyses.")
(license license:asl2.0)))
+
(define-public r-stitch
(package
(name "r-stitch")
generated by cgit v1.2.3 (git 2.47.1) at 2025-03-20 19:24:08 +0000