diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60cf6b7007..1f7972870c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5051,6 +5051,70 @@ two-dimensional genome scans.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public piranha + (package + (name "piranha") + (version "1.1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/smithlabcode/piranha" + "/archive/svn/tags/piranha-" + version ".tar.gz")) + (sha256 + (base32 + "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-smithlab-cpp + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "src/smithlab_cpp") + (for-each (lambda (file) + (install-file file "./src/smithlab_cpp/")) + (find-files (assoc-ref inputs "smithlab-cpp"))) + #t)) + (add-after 'install 'install-to-store + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))) + #:configure-flags + (list (string-append "--with-bam_tools_headers=" + (assoc-ref %build-inputs "bamtools") "/include/bamtools") + (string-append "--with-bam_tools_library=" + (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) + (inputs + `(("bamtools" ,bamtools) + ("samtools" ,samtools-0.1) + ("gsl" ,gsl) + ("smithlab-cpp" + ,(let ((commit "3723e2d")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append "smithlab_cpp-" commit "-checkout")) + (sha256 + (base32 + "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) + (native-inputs + `(("python" ,python-2))) + (home-page "https://github.com/smithlabcode/piranha") + (synopsis "Peak-caller for CLIP-seq and RIP-seq data") + (description + "Piranha is a peak-caller for genomic data produced by CLIP-seq and +RIP-seq experiments. It takes input in BED or BAM format and identifies +regions of statistically significant read enrichment. Additional covariates +may optionally be provided to further inform the peak-calling process.") + (license license:gpl3+))) + (define-public pepr (package (name "pepr") |