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Mon, 12 Nov 2018 22:00:08 +0100 From: pimi Date: Mon, 12 Nov 2018 21:59:49 +0100 Message-ID: <20181112205949.20289-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-24220.002 X-TM-AS-Result: No-7.488800-8.000000-10 X-TMASE-MatchedRID: LvVH+PFvIGh7qToVEfwBPAPZZctd3P4BKx5ICGp/WtHMB0kPsl40w1RE jcghVJrPbXLwY0t0y0CG/0P1OkI4lCVqTewNlt0eu72KpAktHS+usS9CiBzL8SgVbxW7FDOV0jY 9lvMxZvR945fILQVG9xAHcMeOkul1ULNUje/+PyCVOwZbcOalSxvbLpI2wI3oyPRAwD/3abaavg 8fWeMjyX3eWrpAfUW8uNkOvEaew4nXDqWYVB+RWbrbxxduc6FP+nvSwfDbaCXFHcwKL6UE/95IJ 93eYtCx96RcihbwEBwUAF4uBmvRkR8TzIzimOwPwLhRRmviVIVKdDgyPBo71yq2rl3dzGQ1l3+b At/YFVQYDEHUT+FjqwQxYB/SLA9x0rp5hadVHQ9zCQFpAHBy1sWFcyN1Agmm X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.488800-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-24220.002 X-TM-SNTS-SMTP: 2AA8F117650A467CF9149039638DDB272C33C5BB97C4F7B17529E4E68670BBE92000:9 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: ricardo.wurmus@mdc-berlin.de, pimi Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (nanopolish): New variable. --- gnu/packages/bioinformatics.scm | 73 +++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) 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))))