gnu: piranha: Update to 1.2.1.
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
This commit is contained in:
Ricardo Wurmus
parent
fe585be9aa
commit
883302daf2
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@ -5127,68 +5127,71 @@ libraries for systems that do not have these available via other means.")
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(license license:artistic2.0)))
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(define-public piranha
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(package
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(name "piranha")
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(version "1.1.3")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/smithlabcode/piranha"
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"/archive/svn/tags/piranha-"
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version ".tar.gz"))
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(sha256
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(base32
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"1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd"))))
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(build-system gnu-build-system)
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(arguments
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`(#:test-target "test"
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'copy-smithlab-cpp
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(lambda* (#:key inputs #:allow-other-keys)
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(mkdir "src/smithlab_cpp")
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(for-each (lambda (file)
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(install-file file "./src/smithlab_cpp/"))
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(find-files (assoc-ref inputs "smithlab-cpp")))
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#t))
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(add-after 'install 'install-to-store
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin")))
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(mkdir-p bin)
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;; There is no release tarball for the latest version. The latest commit is
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;; older than one year at the time of this writing.
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(let ((revision "1")
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(commit "0466d364b71117d01e4471b74c514436cc281233"))
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(package
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(name "piranha")
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(version (string-append "1.2.1-" revision "." (string-take commit 9)))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/smithlabcode/piranha.git")
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(commit commit)))
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(sha256
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(base32
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"117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
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(build-system gnu-build-system)
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(arguments
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`(#:test-target "test"
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'copy-smithlab-cpp
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(lambda* (#:key inputs #:allow-other-keys)
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(for-each (lambda (file)
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(install-file file bin))
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(find-files "bin" ".*")))
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#t)))
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#:configure-flags
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(list (string-append "--with-bam_tools_headers="
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(assoc-ref %build-inputs "bamtools") "/include/bamtools")
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(string-append "--with-bam_tools_library="
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(assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
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(inputs
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`(("bamtools" ,bamtools)
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("samtools" ,samtools-0.1)
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("gsl" ,gsl)
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("smithlab-cpp"
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,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/smithlabcode/smithlab_cpp.git")
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(commit commit)))
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(file-name (string-append "smithlab_cpp-" commit "-checkout"))
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(sha256
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(base32
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"0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
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(native-inputs
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`(("python" ,python-2)))
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(home-page "https://github.com/smithlabcode/piranha")
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(synopsis "Peak-caller for CLIP-seq and RIP-seq data")
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(description
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"Piranha is a peak-caller for genomic data produced by CLIP-seq and
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(install-file file "./src/smithlab_cpp/"))
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(find-files (assoc-ref inputs "smithlab-cpp")))
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#t))
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(add-after 'install 'install-to-store
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin")))
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(mkdir-p bin)
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(for-each (lambda (file)
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(install-file file bin))
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(find-files "bin" ".*")))
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#t)))
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#:configure-flags
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(list (string-append "--with-bam_tools_headers="
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(assoc-ref %build-inputs "bamtools") "/include/bamtools")
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(string-append "--with-bam_tools_library="
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(assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
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(inputs
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`(("bamtools" ,bamtools)
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("samtools" ,samtools-0.1)
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("gsl" ,gsl)
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("smithlab-cpp"
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,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/smithlabcode/smithlab_cpp.git")
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(commit commit)))
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(file-name (string-append "smithlab_cpp-" commit "-checkout"))
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(sha256
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(base32
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"0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
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(native-inputs
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`(("python" ,python-2)))
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(home-page "https://github.com/smithlabcode/piranha")
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(synopsis "Peak-caller for CLIP-seq and RIP-seq data")
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(description
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"Piranha is a peak-caller for genomic data produced by CLIP-seq and
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RIP-seq experiments. It takes input in BED or BAM format and identifies
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regions of statistically significant read enrichment. Additional covariates
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may optionally be provided to further inform the peak-calling process.")
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(license license:gpl3+)))
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(license license:gpl3+))))
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(define-public pepr
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(package
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