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01/02: gnu: nanopolish: Update to 0.14.0.
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From: |
guix-commits |
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Subject: |
01/02: gnu: nanopolish: Update to 0.14.0. |
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Date: |
Fri, 6 Jan 2023 09:01:44 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 24e5dbb57ad39cd057317319b8695f70111faa04
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Jan 6 14:51:55 2023 +0100
gnu: nanopolish: Update to 0.14.0.
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.
---
gnu/packages/bioinformatics.scm | 160 ++++++++++++++++++++--------------------
1 file changed, 79 insertions(+), 81 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index be5d0bbada..e3860ca45f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14358,91 +14358,89 @@ choosing which reads pass the filter.")
license:asl2.0))))) ;histogram.py
(define-public nanopolish
- ;; The recommended way to install is to clone the git repository
- ;; <https://github.com/jts/nanopolish#installing-a-particular-release>.
- ;; Also, the differences between release and current version seem to be
- ;; significant.
- (let ((commit "6331dc4f15b9dfabb954ba3fae9d76b6c3ca6377")
- (revision "1"))
- (package
- (name "nanopolish")
- (version (git-version "0.11.1" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/jts/nanopolish";)
- (commit commit)
- (recursive? #t)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "15ikl3d37y49pwd7vx36xksgsqajhf24q7qqsnpl15dqqyy5qgbc"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (delete-file-recursively "htslib")
- #t))))
- (build-system gnu-build-system)
- (arguments
- `(#:make-flags
- `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
- #:tests? #f ; no check target
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'find-eigen
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "CPATH"
- (string-append
- (search-input-directory inputs "/include/eigen3")
- ":" (or (getenv "CPATH") "")))))
- (delete 'configure)
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin"))
- (scripts (string-append out
"/share/nanopolish/scripts")))
+ (package
+ (name "nanopolish")
+ (version "0.14.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jts/nanopolish";)
+ (commit (string-append "v" version))
+ (recursive? #t)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1ha9v5ia0qrwgav0956cfc7n64wjm9a9w3rvkg21g37a994yixg5"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; TODO: unbundle slow5lib
+ '(begin (for-each delete-file-recursively
+ '("htslib" "minimap2"))))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:make-flags
+ #~(list "HDF5=noinstall"
+ "EIGEN=noinstall"
+ "HTS=noinstall"
+ "MINIMAP2=noinstall"
+ (string-append "CC=" #$(cc-for-target)))
+ #:tests? #f ; no check target
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'find-eigen
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "CPATH"
+ (string-append
+ (search-input-directory inputs "/include/eigen3")
+ ":" (or (getenv "CPATH") "")))))
+ (delete 'configure)
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin"))
+ (scripts (string-append #$output
"/share/nanopolish/scripts")))
- (install-file "nanopolish" bin)
- (for-each (lambda (file) (install-file file scripts))
- (find-files "scripts" ".*"))
- #t)))
- (add-after 'install 'wrap-programs
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((pythonpath (getenv "GUIX_PYTHONPATH"))
- (perl5lib (getenv "PERL5LIB"))
- (scripts (string-append (assoc-ref outputs "out")
- "/share/nanopolish/scripts"))
- (guile (search-input-file inputs "bin/guile")))
- (for-each (lambda (file)
- (wrap-program file `("GUIX_PYTHONPATH" ":" prefix
(,pythonpath))))
- (find-files scripts "\\.py"))
- (for-each (lambda (file)
- (wrap-script file #:guile guile
- `("PERL5LIB" ":" prefix
(,perl5lib))))
- (find-files scripts "\\.pl"))))))))
- (inputs
- `(("guile" ,guile-3.0) ; for wrappers
- ("eigen" ,eigen)
- ("hdf5" ,hdf5)
- ("htslib" ,htslib)
- ("perl" ,perl)
- ("bioperl" ,bioperl-minimal)
- ("perl-getopt-long" ,perl-getopt-long)
- ("python" ,python-wrapper)
- ("python-biopython" ,python-biopython)
- ("python-numpy" ,python-numpy)
- ("python-pysam" ,python-pysam)
- ("python-scikit-learn" , python-scikit-learn)
- ("python-scipy" ,python-scipy)
- ("zlib" ,zlib)))
- (home-page "https://github.com/jts/nanopolish";)
- (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
- (description
- "This package analyses the Oxford Nanopore sequencing data at
signal-level.
+ (install-file "nanopolish" bin)
+ (for-each (lambda (file) (install-file file scripts))
+ (find-files "scripts" ".*")))))
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((pythonpath (getenv "GUIX_PYTHONPATH"))
+ (perl5lib (getenv "PERL5LIB"))
+ (scripts (string-append #$output
"/share/nanopolish/scripts"))
+ (guile (search-input-file inputs "bin/guile")))
+ (for-each (lambda (file)
+ (wrap-program file `("GUIX_PYTHONPATH" ":" prefix
(,pythonpath))))
+ (find-files scripts "\\.py"))
+ (for-each (lambda (file)
+ (wrap-script file #:guile guile
+ `("PERL5LIB" ":" prefix (,perl5lib))))
+ (find-files scripts "\\.pl"))))))))
+ (inputs
+ `(("guile" ,guile-3.0) ; for wrappers
+ ("eigen" ,eigen)
+ ("hdf5" ,hdf5)
+ ("htslib" ,htslib)
+ ("minimap2" ,minimap2)
+ ("perl" ,perl)
+ ("bioperl" ,bioperl-minimal)
+ ("perl-getopt-long" ,perl-getopt-long)
+ ("python" ,python-wrapper)
+ ("python-biopython" ,python-biopython)
+ ("python-numpy" ,python-numpy)
+ ("python-pysam" ,python-pysam)
+ ("python-scikit-learn" , python-scikit-learn)
+ ("python-scipy" ,python-scipy)
+ ("zlib" ,zlib)))
+ (native-inputs (list cmake-minimal))
+ (home-page "https://github.com/jts/nanopolish";)
+ (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
+ (description
+ "This package analyses the Oxford Nanopore sequencing data at
signal-level.
Nanopolish can calculate an improved consensus sequence for a draft genome
assembly, detect base modifications, call SNPs (Single nucleotide
polymorphisms) and indels with respect to a reference genome and more.")
- (license license:expat))))
+ (license license:expat)))
(define-public cnvkit
(package