diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 160 |
1 files 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 |