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Wed, 11 Jan 2023 05:47:51 -0800 (PST) From: zimoun Date: Wed, 11 Jan 2023 14:47:44 +0100 Message-Id: <20230111134744.2551087-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Received-SPF: pass client-ip=2a00:1450:4864:20::32d; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32d.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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 From: Simon Tournier * gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. --- gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) base-commit: a8b2decf287498eeb51ef23712c5bd01b60cb18b diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..4ef9ec15b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li -;;; Copyright © 2021, 2022 Simon Tournier +;;; Copyright © 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2022 Navid Afkhami ;;; Copyright © 2022 Antero Mejr @@ -512,6 +512,48 @@ (define-public bedtools-2.18 (inputs (list samtools zlib)))) +(define-public cellsnp-lite + ;; Last release from November 2021 and does not contain fixes. + (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") + (revision "0")) + (package + (name "cellsnp-lite") + (version (git-version "1.2.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/single-cell-genetics/cellsnp-lite") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags #~(list (string-append "--with-htslib=" + #$(this-package-input "htslib"))))) + (inputs + (list curl + htslib + openssl + zlib)) + (native-inputs + (list autoconf)) + (home-page "https://cellsnp-lite.readthedocs.io") + (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data") + (description + "This package is designed to pileup the expressed alleles in +single-cell or bulk RNA-seq data, which can be directly used for donor +deconvolution in multiplexed single-cell RNA-seq data, particularly with other +packages, which assigns cells to donors and detects doublets as vireo, even +without genotyping reference. + +This package is the C version of the deprecated cellSNP implemented in Python. +Comparedto cellSNP, this package is more efficient with higher speed and less +memory usage.") + (license license:asl2.0)))) + (define-public pbcopper (package (name "pbcopper")