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[66.158.149.239]) by smtp.gmail.com with ESMTPSA id 2-20020ac82082000000b002f39b99f672sm4287690qtd.12.2022.05.14.21.47.09 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 May 2022 21:47:09 -0700 (PDT) From: Maxim Cournoyer Date: Sun, 15 May 2022 00:36:50 -0400 Message-Id: <20220515044629.6843-23-maxim.cournoyer@gmail.com> X-Mailer: git-send-email 2.36.0 In-Reply-To: <20220515044629.6843-1-maxim.cournoyer@gmail.com> References: <20220515044629.6843-1-maxim.cournoyer@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1652591237; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=c2TxSIj5YOiIhhze9ClZbAsl8hKnP/JSHj4gLsH0Gs4=; b=TSxA97Qm+62JV6y9ilXZeP68lVgi2y4ARiQu6MTjzxcqXJAH4pmPloeKdVG0cWV95Nhmdm TYCQ4GtMf1CpkuQS+bZ8Thxlk6hPk4Pl7wVlo6fvX+UDlU9HdLiX/379g7WktV1hxE+cAh TVnfGoOtpb3zTkbUh6DlFgxIe88tZ7kpFmQPqdWb+X2x8qD4lT3n9g4ftVHSoWo/XsCj+H +zsFPzrUYDCefgx5O/FL5aZ91+fwGXTftA6DWnJKaOtjidHB40gAEXYRRz0s6JUrqYhgyZ PC1Lx039HuffKCmcR3gIUcAiC4bWpoVqGn8J1OqCGf67cMTzmg00ESdSz0dakQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652591237; a=rsa-sha256; cv=none; b=lJx0obTzaQjOzeePzYlSycMsKXSGqEGMz7+tEsYQNUGd4BTMQLig56b7JeWcxCwNGfk04N 6JOc1YK8y60hULqg7hPvjYr0pdsiz4NvfE6NHJg1Go3B9XTSMbp7Gl59vZwQ8GvZE3I31S n2QPQwRGsp67JXXvM7XEjlwQ6ijH/nU5WW6oWgqS5VL8k1RTd317/wSFcRv/gKLQhU8N52 pF3EMall0objKcmuVhDrTob++HDA7oc+IiUCfOvl15W+wmdRXjpO7ZAvv9CBN1kps0TBlM IXpFwaWEp3D95IPuOzVYnuJ8THtv5qI5nbTGpQdeoDJgXGtIO0dB90p9i3XVBw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b="V/diTMJX"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.17 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b="V/diTMJX"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 57CB01B1D6 X-Spam-Score: 6.17 X-Migadu-Scanner: scn0.migadu.com X-TUID: mdWXfeX3pU6t * gnu/packages/bioinformatics.scm (bamm): Delete variable. --- gnu/packages/bioinformatics.scm | 79 --------------------------------- 1 file changed, 79 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9d4fcbb188..5f637fe29a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -210,85 +210,6 @@ (define-public aragorn structure of the predicted RNA.") (license license:gpl2))) -(define-public bamm - (package - (name "bamm") - (version "1.7.3") - (source (origin - (method git-fetch) - ;; BamM is not available on pypi. - (uri (git-reference - (url "https://github.com/Ecogenomics/BamM") - (commit version) - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) - (modules '((guix build utils))) - (snippet - `(begin - ;; Delete bundled htslib. - (delete-file-recursively "c/htslib-1.3.1"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; BamM is Python 2 only. - ;; Do not use bundled libhts. Do use the bundled libcfu because it has - ;; been modified from its original form. - #:configure-flags - ,#~(let ((htslib #$(this-package-input "htslib"))) - (list "--with-libhts-lib" (string-append htslib "/lib") - "--with-libhts-inc" (string-append htslib "/include/htslib"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ - (with-directory-excursion "c" - (let ((sh (which "sh"))) - (for-each make-file-writable (find-files "." ".*")) - ;; Use autogen so that 'configure' works. - (substitute* "autogen.sh" (("/bin/sh") sh)) - (setenv "CONFIG_SHELL" sh) - (invoke "./autogen.sh"))))) - (delete 'build) ;the build loops otherwise - (replace 'check - (lambda _ - ;; There are 2 errors printed, but they are safe to ignore: - ;; 1) [E::hts_open_format] fail to open file ... - ;; 2) samtools view: failed to open ... - (invoke "nosetests"))) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PATH")) - (pythonpath (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/bamm") - `("PATH" ":" prefix (,path)) - `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) - (native-inputs - (list autoconf - automake - libtool - zlib - python2-nose - python2-pysam)) - (inputs - (list htslib-1.3 ; At least one test fails on htslib-1.4+. - samtools - bwa - grep - sed - coreutils)) - (propagated-inputs - (list python2-numpy)) - (home-page "https://ecogenomics.github.io/BamM/") - (synopsis "Metagenomics-focused BAM file manipulator") - (description - "BamM is a C library, wrapped in python, to efficiently generate and -parse BAM files, specifically for the analysis of metagenomic data. For -instance, it implements several methods to assess contig-wise read coverage.") - (license license:lgpl3+))) - (define-public bamtools (package (name "bamtools") -- 2.36.0