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.master
Ricardo Wurmus
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8ace894681
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24e5dbb57a
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@ -14358,91 +14358,89 @@ choosing which reads pass the filter.")
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license:asl2.0))))) ;histogram.py
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(define-public nanopolish
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;; The recommended way to install is to clone the git repository
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;; <https://github.com/jts/nanopolish#installing-a-particular-release>.
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;; Also, the differences between release and current version seem to be
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;; significant.
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(let ((commit "6331dc4f15b9dfabb954ba3fae9d76b6c3ca6377")
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(revision "1"))
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(package
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(name "nanopolish")
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(version (git-version "0.11.1" revision commit))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/jts/nanopolish")
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(commit commit)
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(recursive? #t)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "15ikl3d37y49pwd7vx36xksgsqajhf24q7qqsnpl15dqqyy5qgbc"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(delete-file-recursively "htslib")
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(#:make-flags
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`("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
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#:tests? #f ; no check target
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'find-eigen
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "CPATH"
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(string-append
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(search-input-directory inputs "/include/eigen3")
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":" (or (getenv "CPATH") "")))))
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(delete 'configure)
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(scripts (string-append out "/share/nanopolish/scripts")))
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(package
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(name "nanopolish")
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(version "0.14.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/jts/nanopolish")
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(commit (string-append "v" version))
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(recursive? #t)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1ha9v5ia0qrwgav0956cfc7n64wjm9a9w3rvkg21g37a994yixg5"))
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(modules '((guix build utils)))
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(snippet
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;; TODO: unbundle slow5lib
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'(begin (for-each delete-file-recursively
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'("htslib" "minimap2"))))))
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(build-system gnu-build-system)
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(arguments
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(list
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#:make-flags
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#~(list "HDF5=noinstall"
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"EIGEN=noinstall"
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"HTS=noinstall"
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"MINIMAP2=noinstall"
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(string-append "CC=" #$(cc-for-target)))
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#:tests? #f ; no check target
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'find-eigen
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "CPATH"
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(string-append
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(search-input-directory inputs "/include/eigen3")
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":" (or (getenv "CPATH") "")))))
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(delete 'configure)
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(replace 'install
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(lambda _
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(let ((bin (string-append #$output "/bin"))
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(scripts (string-append #$output "/share/nanopolish/scripts")))
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(install-file "nanopolish" bin)
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(for-each (lambda (file) (install-file file scripts))
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(find-files "scripts" ".*"))
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#t)))
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(add-after 'install 'wrap-programs
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((pythonpath (getenv "GUIX_PYTHONPATH"))
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(perl5lib (getenv "PERL5LIB"))
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(scripts (string-append (assoc-ref outputs "out")
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"/share/nanopolish/scripts"))
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(guile (search-input-file inputs "bin/guile")))
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(for-each (lambda (file)
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(wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))
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(find-files scripts "\\.py"))
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(for-each (lambda (file)
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(wrap-script file #:guile guile
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`("PERL5LIB" ":" prefix (,perl5lib))))
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(find-files scripts "\\.pl"))))))))
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(inputs
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`(("guile" ,guile-3.0) ; for wrappers
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("eigen" ,eigen)
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("hdf5" ,hdf5)
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("htslib" ,htslib)
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("perl" ,perl)
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("bioperl" ,bioperl-minimal)
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("perl-getopt-long" ,perl-getopt-long)
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("python" ,python-wrapper)
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("python-biopython" ,python-biopython)
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("python-numpy" ,python-numpy)
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("python-pysam" ,python-pysam)
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("python-scikit-learn" , python-scikit-learn)
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("python-scipy" ,python-scipy)
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("zlib" ,zlib)))
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(home-page "https://github.com/jts/nanopolish")
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(synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
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(description
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"This package analyses the Oxford Nanopore sequencing data at signal-level.
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(install-file "nanopolish" bin)
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(for-each (lambda (file) (install-file file scripts))
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(find-files "scripts" ".*")))))
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(add-after 'install 'wrap-programs
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((pythonpath (getenv "GUIX_PYTHONPATH"))
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(perl5lib (getenv "PERL5LIB"))
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(scripts (string-append #$output "/share/nanopolish/scripts"))
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(guile (search-input-file inputs "bin/guile")))
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(for-each (lambda (file)
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(wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))
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(find-files scripts "\\.py"))
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(for-each (lambda (file)
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(wrap-script file #:guile guile
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`("PERL5LIB" ":" prefix (,perl5lib))))
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(find-files scripts "\\.pl"))))))))
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(inputs
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`(("guile" ,guile-3.0) ; for wrappers
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("eigen" ,eigen)
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("hdf5" ,hdf5)
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("htslib" ,htslib)
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("minimap2" ,minimap2)
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("perl" ,perl)
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("bioperl" ,bioperl-minimal)
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("perl-getopt-long" ,perl-getopt-long)
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("python" ,python-wrapper)
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("python-biopython" ,python-biopython)
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("python-numpy" ,python-numpy)
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("python-pysam" ,python-pysam)
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("python-scikit-learn" , python-scikit-learn)
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("python-scipy" ,python-scipy)
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("zlib" ,zlib)))
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(native-inputs (list cmake-minimal))
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(home-page "https://github.com/jts/nanopolish")
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(synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
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(description
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"This package analyses the Oxford Nanopore sequencing data at signal-level.
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Nanopolish can calculate an improved consensus sequence for a draft genome
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assembly, detect base modifications, call SNPs (Single nucleotide
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polymorphisms) and indels with respect to a reference genome and more.")
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(license license:expat))))
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(license license:expat)))
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(define-public cnvkit
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(package
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