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[85.239.161.196]) by smtp.gmail.com with ESMTPSA id f23-20020a17090631d700b007ba9c181202sm6033908ejf.56.2023.01.11.03.00.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 11 Jan 2023 03:00:17 -0800 (PST) From: Raoul Jean Piere Bonnal Date: Sat, 7 Jan 2023 15:39:20 +0100 Message-Id: <46f5cd81bff5fdde4a3a086c76cd2e2b41bfac36.1673102355.git.science.raoul.bonnal@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Received-SPF: pass client-ip=2a00:1450:4864:20::636; envelope-from=science.raoul.bonnal@gmail.com; helo=mail-ej1-x636.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Wed, 11 Jan 2023 06:12:45 -0500 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Wed, 11 Jan 2023 08:18:35 -0500 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches --- gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) base-commit: 24ad9a9a48ca4f51505912224217a2a9688c7fa0 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..3b9c135c2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3547,6 +3547,63 @@ (define-public discrover of nucleic acid binding proteins.") (license license:gpl3+))) +(define-public eagle + (let ((commit "b8b3ae205d5f9faf99f231fe7d02ae51eaca2f8b") + (revision "1")) + (package + (name "eagle") + (version "2.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/poruloh/Eagle") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1pylmn3yqimq85fnqw7m702zqp4bw4bw60b2pf0xm2yh1w9grzss")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "src/Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("BLAS_DIR = .*") "") + (("BOOST_INSTALL_DIR = .*") "") + (("HTSLIB_DIR = .*") "") + (("ZLIB_STATIC_DIR = .*") "") + (("LIBSTDCXX_STATIC_DIR = .*") "") + (("GLIBC_STATIC_DIR = .*") "")))))) + (properties `((upstream-name . "Eagle"))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:parallel-build? #f + #:make-flags ,#~(list (string-append "-C" "src/")) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + ;; The package's Makefile doesn't provide and "install" + ;; rule so di it by ourselves. + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (install-file "src/eagle" bin))))))) + (inputs + (list boost + openblas + htslib)) + (home-page "https://alkesgroup.broadinstitute.org/Eagle/") + (synopsis "Statistical estimation of haplotypes from genotype data") + (description "Eagle estimates haplotype phase either within a genotyped +cohort or using a phased reference panel. It uses a very fast HMM-based algorithm +that improves speed and accuracy over existing methods via two key ideas: a new data +structure based on the positional Burrows-Wheeler transform and a rapid search +algorithm that explores only the most relevant paths through the HMM. It supports +phasing sequence data with or without a reference and also supports phasing chrX.") + (license license:gpl3+)))) + (define-public eigensoft (package (name "eigensoft")