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[66.158.149.239]) by smtp.gmail.com with ESMTPSA id 2-20020ac82082000000b002f39b99f672sm4287690qtd.12.2022.05.14.21.47.06 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 May 2022 21:47:06 -0700 (PDT) From: Maxim Cournoyer Date: Sun, 15 May 2022 00:36:46 -0400 Message-Id: <20220515044629.6843-19-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=1652590771; 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=oYQ+cUN+k07LitRymNjzaaOAe3ozBr/0MO02sJbRG3k=; b=ElaOg+wbFiuHeliWg+5wjDi5cm3G6iSB69vbHYoN9fRKF1PqVBvP8MNOPfRxas8rxeuWaD N9NAHoAaHH/BtRpMF/ARWNiGI1n3F28GCG3mvH9Q7qqs/W75mgsdP0XhYJ63KiJKTmgHKp P4XaFGrvobEAOHvznMjd03x3v+w9DZuJt0E4uMaNB97pL+HsLu1c7dZNqXJagmX47sOUZk gBRcxDUJ+Vt/nD+SKb811+hR6V+CBhxMNe840TZnMyovj7HwwbDjmVdYOog0vVYyRxPRvY FJFaEfNdXqgWqkdZQlhlmqGriaDAD5pW66BmWS9wFYkuN64XF2gcd9WiBr4PSg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652590771; a=rsa-sha256; cv=none; b=TVdehXJfCQUkCatiDHRZjAfRu+FjhXw4Q4RLZTyPp0r5l3ktGqbL5SZ8v5GvXPNnkUky9U lbgyP8PeVaKgTITkwQIdxI1VB1mr3FiLfE/8QU+kY+FaotXtf4vzORhalxXeZVkuIR/s89 iyLfDLkJzfpMjhZI0ATwdAtcBrm+i4adFKvEzknb0NlQIa35ZB4PiwMIaRZc0ffvEa/3Pe UyxncFCAjhSxx6su29B5EbomvZlfMfFxsYkg7euA6eAD/S4Ki4OlwZC62JyIlL3uG1iGbd qAO6fhK/DFxiyntR2ncUjrWzL0KJPdPXYOs5X57kwQCMhm3rUb3enxsu94aJcg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=QF8h7efq; 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: 6.47 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=QF8h7efq; 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: A1FC92B634 X-Spam-Score: 6.47 X-Migadu-Scanner: scn1.migadu.com X-TUID: zMVCoScUTRhA * gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b. [python]: Delete argument. [phases]: Delete trailing #t. {make-writable}: Delete phase. {adjust-requirements}: New phase. {patch-invocations}: Use search-input-file. {wrap-program}: Use search-input-file. [inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam. [home-page]: Update URL. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++---------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8b9c8c65c2..72d033888f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2390,59 +2390,60 @@ (define-public python-plastid (define-public tetoolkit (package (name "tetoolkit") - (version "2.0.3") + (version "2.2.1b") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mhammell-laboratory/tetoolkit") + (url "https://github.com/mhammell-laboratory/TEtranscripts") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807")))) + "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; not guaranteed to work with Python 3 - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'make-writable + (add-after 'unpack 'adjust-requirements (lambda _ - (for-each make-file-writable (find-files ".")) - #t)) + (substitute* "setup.py" + ;; This defunct dependency isn't required for Python 3 (see: + ;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111). + ((".*'argparse'.*") "")))) (add-after 'unpack 'patch-invocations (lambda* (#:key inputs #:allow-other-keys) (substitute* '("bin/TEtranscripts" "bin/TEcount") (("'sort ") - (string-append "'" (which "sort") " ")) + (string-append "'" (search-input-file inputs "bin/sort") " ")) (("'rm -f ") - (string-append "'" (which "rm") " -f ")) - (("'Rscript'") (string-append "'" (which "Rscript") "'"))) + (string-append "'" (search-input-file inputs "bin/rm") " -f ")) + (("'Rscript'") + (string-append "'" (search-input-file inputs "bin/Rscript") + "'"))) (substitute* "TEToolkit/IO/ReadInputs.py" - (("BamToBED") (which "bamToBed"))) + (("BamToBED") + (search-input-file inputs "bin/bamToBed"))) (substitute* "TEToolkit/Normalization.py" (("\"Rscript\"") - (string-append "\"" (which "Rscript") "\""))) - #t)) + (string-append "\"" (search-input-file inputs "bin/Rscript") + "\""))))) (add-after 'install 'wrap-program (lambda* (#:key outputs #:allow-other-keys) ;; Make sure the executables find R packages. - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (script) - (wrap-program (string-append out "/bin/" script) - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) - '("TEtranscripts" - "TEcount"))) - #t))))) + (for-each (lambda (script) + (wrap-program script + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + (list (search-input-file outputs "bin/TEtranscripts") + (search-input-file outputs "bin/TEcount")))))))) (inputs - (list coreutils + (list bash-minimal + coreutils bedtools - python2-argparse - python2-pysam + python-pysam r-minimal r-deseq2)) - (home-page "https://github.com/mhammell-laboratory/tetoolkit") + (home-page "https://github.com/mhammell-laboratory/TEtranscripts") (synopsis "Transposable elements in differential enrichment analysis") (description "This is package for including transposable elements in differential -- 2.36.0