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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161583177318456 (code B ref 47171); Mon, 15 Mar 2021 18:10:05 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:33 +0000 Received: from localhost ([127.0.0.1]:36959 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrem-0004nV-Vu for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:33 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:36145) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLreh-0004lc-4D for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:27 -0400 Received: by mail-wr1-f41.google.com with SMTP id y16so9183123wrw.3 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:27 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=D6JehzIlOTQUoVLz4lMMYKkMox6+bUZVl33d8isFOQo=; b=EzQCRZhnT2Pr+bpUZuoIZba209tAUVt35a+F68li4nP+R7TEzn4LheFkM7J1YDRwe4 Lr3Y4LG3750UUGfOVnJirMNMH76Yc/JtBWmgFHnpkIHIm+GaLpbva/XZwNmXORGeEQt0 yDhMIgksw3s4YUvCe+vkYZTYUDeg0Se74PJ5ubfojeqtGVAGunDAEX2S/kCBSeWB8C25 Licw+YlO4gtA65Kca7HfC8W+rB8uObBbVi31VxUunO9KZ7zoqDbjWkgrBAv9q71jWdjA 2CPPB31KORoixmA9weo33yTEPb08GayK/Ir+sUYDeIeLmvgQ55M2IPYc5BFyr6nNjwLL fBjw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=D6JehzIlOTQUoVLz4lMMYKkMox6+bUZVl33d8isFOQo=; b=JNhaLE/wx+wJUeQa7fmqx0uD0+1F+o4WhkK/YlsPgGTwelzWUoSSimyEeHlpNfaF1F cbxsuEgssPV+Uiqt4f8PMdWDay6QFZvdYFRvhA1TtnSyjhm9bEKMRmSnA9MBCsjWoQv7 hvK0djOs5Vva0uGgytIZH22u+5O3jEb9q8XMcK7+MR1lP0kgJ8Jrdh80TI6+LEtULh5W iynU7JvUmxjhKSbmDfkcXo+eGLm5MP/XnHqzEfbeNu+HmLftFN5kljg3sdbGXRFE5HgV RvuDSpUjlO6zw9G6kyxuGaJOZjKQPnfdCp1fbr/inqkAeyZb9M+d956sPevVPyofxHIB q5VQ== X-Gm-Message-State: AOAM531aN8aZgbNq6eJASfriRQjXUU+X0uTPyHXtMpivgZvfgJWTPFJS V+8m9qg7zRll67Qlh+yAe6ba60u2p2s= X-Google-Smtp-Source: ABdhPJyTvoTQhWO7SpRYejaZUg3/cj9psNeH4krBWYijn3HzcoIIY9Hid8wJIwAgmHsdlL9jo2t+Ug== X-Received: by 2002:adf:f44b:: with SMTP id f11mr860316wrp.345.1615831761634; Mon, 15 Mar 2021 11:09:21 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.21 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:21 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:03 +0100 Message-Id: <20210315180904.8346-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315180904.8346-1-zimon.toutoune@gmail.com> References: <20210315180904.8346-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b7d65023d..c659bdd09e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 415210085e..05805d1a8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,49 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rsamtools - (package - (name "r-rsamtools") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Rsamtools" version)) - (sha256 - (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) - (properties - `((upstream-name . "Rsamtools"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") - (synopsis "Interface to samtools, bcftools, and tabix") - (description - "This package provides an interface to the @code{samtools}, -@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence -Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed -tab-delimited (tabix) files.") - (license license:expat))) - (define-public r-delayedarray (package (name "r-delayedarray")