pimi wrote 6 years ago
(address . guix-patches@gnu.org)(address . ricardo.wurmus@mdc-berlin.de)(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)
20181112205949.20289-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (nanopolish): New variable.
---
gnu/packages/bioinformatics.scm | 73 +++++++++++++++++++++++++++++++++
1 file changed, 73 insertions(+)
Toggle diff (83 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf49f4e1d..fa1a91a22 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14282,3 +14282,76 @@ 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 seems to be significative
+ (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.")
+ ;; for auxiliary scripts is not mentioned any license
+ (license license:expat))))
--
2.17.1