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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 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 (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