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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 74 |
1 files changed, 74 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1a7199241a..dc36cedb0c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14362,3 +14362,77 @@ both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.") (license (list license:gpl3 ;filtlong 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 "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d") + (revision "1")) + (package + (name "nanopolish") + (version (git-version "0.10.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jts/nanopolish.git") + (commit commit) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")))) + (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 (assoc-ref inputs "eigen") + "/include/eigen3")) + #t)) + (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"))) + + (install-file "nanopolish" bin) + (for-each (lambda (file) (install-file file scripts)) + (find-files "scripts" ".*")) + #t))) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + (for-each (lambda (file) + (wrap-program file `("PYTHONPATH" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.py")) + (for-each (lambda (file) + (wrap-program file `("PERL5LIB" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.pl")) + #t))))) + (inputs + `(("eigen" ,eigen) + ("hdf5" ,hdf5) + ("htslib" ,htslib) + ("perl" ,perl) + ("python" ,python) + ("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. +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)))) |