From patchwork Fri Jul 2 10:06:14 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: M X-Patchwork-Id: 30902 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 07AB527BC81; Fri, 2 Jul 2021 11:10:04 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, FREEMAIL_FROM,MAILING_LIST_MULTI,SPF_HELO_PASS,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 4491E27BC78 for ; Fri, 2 Jul 2021 11:10:03 +0100 (BST) Received: from localhost ([::1]:58246 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lzG7W-0008WM-80 for patchwork@mira.cbaines.net; Fri, 02 Jul 2021 06:10:02 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50828) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lzG6x-0007i6-8Q for guix-patches@gnu.org; Fri, 02 Jul 2021 06:09:27 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51308) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lzG6w-0004XG-VZ for guix-patches@gnu.org; Fri, 02 Jul 2021 06:09:27 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lzG6w-0008R3-QM for guix-patches@gnu.org; Fri, 02 Jul 2021 06:09:26 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49327] [PATCH core-updates 008/128] gnu: bioinformatics: Add 'bash' input for 'wrap-program'. Resent-From: Maxime Devos Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 02 Jul 2021 10:09:26 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49327 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49327@debbugs.gnu.org Cc: Maxime Devos Received: via spool by 49327-submit@debbugs.gnu.org id=B49327.162522056232303 (code B ref 49327); Fri, 02 Jul 2021 10:09:26 +0000 Received: (at 49327) by debbugs.gnu.org; 2 Jul 2021 10:09:22 +0000 Received: from localhost ([127.0.0.1]:34582 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lzG6o-0008Nu-HO for submit@debbugs.gnu.org; Fri, 02 Jul 2021 06:09:21 -0400 Received: from laurent.telenet-ops.be ([195.130.137.89]:60282) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lzG6G-0008Bx-WA for 49327@debbugs.gnu.org; Fri, 02 Jul 2021 06:08:53 -0400 Received: from localhost.localdomain ([213.119.233.144]) by laurent.telenet-ops.be with bizsmtp id QA8h2500B37benp01A8kBz; Fri, 02 Jul 2021 12:08:44 +0200 From: Maxime Devos Date: Fri, 2 Jul 2021 12:06:14 +0200 Message-Id: <20210702100814.23249-8-maximedevos@telenet.be> X-Mailer: git-send-email 2.32.0 In-Reply-To: <20210702100814.23249-1-maximedevos@telenet.be> References: <20210702100814.23249-1-maximedevos@telenet.be> MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r21; t=1625220524; bh=7HhOn1LfdjyHMXUkmXcrJTiX3Tco3ZjoBAIRek+UOVE=; h=From:To:Cc:Subject:Date:In-Reply-To:References; b=nkA1Fkha4rdG0R/MG/12Ky9ApJX26vsuTapeCfcAQJ65j53p1UQJ+EtgcVt8kGjxA aPo3cShE/Ati4MyHo7HpcxOmHpksMmSZslhVxYjwOTBLUfpCOgA7J4ekv4+27PY7zw JQdyq4nKvrGD2AHP4D4yNWAQQOhNoQ1xE6ZWNNW+IIn7agiWnASDdyuQQjIzrioNan 8korNOkLnO1/5wnJFJyU9GQaQpm3gmKF7w04vICtHC5lJYKMHQDI52I6CkN2gGnMQg z9Zg7925vrv7/PKd9JWPkltGx4uWnOm7hHFO06/x20iXGFoHsHHcIG+1PYTaQnKAjU vhZVM6XKdebcg== 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 It is required for cross-compilation. * gnu/packages/bioinformatics.scm (bamm)[inputs]: Add 'bash-minimal'. (ribotaper)[inputs]: Likewise. (bioperl-minimal)[inputs]: Likewise. (tetoolkit)[inputs]: Likewise. (couger)[inputs]: Likewise. (repeat-masker)[inputs]: Likewise. (edirect)[inputs]: Likewise. (mafft)[inputs]: Likewise. (prank)[inputs]: Likewise. (roary)[inputs]: Likewise. (rsem)[inputs]: Likewise. (shorah)[inputs]: Likewise. (rcas-web)[inputs]: Likewise. (filtlong)[inputs]: Likewise. (nanopolish)[inputs]: Likewise. (find-circ)[inputs]: Likewise. (arriba)[inputs]: Likewise. (pplacer-scripts)[inputs]: Likewise. (ensembl-vep)[inputs]: Likewise. --- gnu/packages/bioinformatics.scm | 54 ++++++++++++++++++++++----------- 1 file changed, 37 insertions(+), 17 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 64fc6173db..6af530298c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -263,6 +263,7 @@ structure of the predicted RNA.") (inputs `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. ("samtools" ,samtools) + ("bash" ,bash-minimal) ; for wrap-program ("bwa" ,bwa) ("grep" ,grep) ("sed" ,sed) @@ -757,7 +758,8 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " "Ribotaper.sh"))) #t))))) (inputs - `(("bedtools" ,bedtools-2.18) + `(("bash" ,bash-minimal) ; for wrap-program + ("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) ("r-minimal" ,r-minimal) ("r-foreach" ,r-foreach) @@ -1166,7 +1168,9 @@ alignments and perform the following operations: `("PERL5LIB" ":" prefix (,path)))) (find-files bin "\\.pl$")) #t)))))) - (inputs inputs) + (inputs + `(("bash" ,bash-minimal) ; for wrap-program + ,@inputs)) (native-inputs `(("perl-test-most" ,perl-test-most))) (home-page "https://metacpan.org/release/BioPerl") @@ -2226,6 +2230,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") #t))))) (inputs `(("coreutils" ,coreutils) + ("bash" ,bash-minimal) ; for wrap-program ("bedtools" ,bedtools) ("python-argparse" ,python2-argparse) ("python-pysam" ,python2-pysam) @@ -2423,7 +2428,8 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") `("GUIX_PYTHONPATH" ":" prefix (,path)))) #t))))) (inputs - `(("python" ,python-2) + `(("bash" ,bash-minimal) ; for wrap-program + ("python" ,python-2) ("python2-pillow" ,python2-pillow) ("python2-numpy" ,python2-numpy) ("python2-scipy" ,python2-scipy) @@ -3001,7 +3007,8 @@ bases are detected.") (wrap-program (string-append bin "/RepeatMasker") `("PERL5LIB" ":" prefix (,path ,share))))))))) (inputs - `(("perl" ,perl) + `(("bash" ,bash-minimal) ; for wrap-program + ("perl" ,perl) ("perl-text-soundex" ,perl-text-soundex) ("python" ,python) ("python-h5py" ,python-h5py) @@ -3255,7 +3262,8 @@ quantitative phenotypes.") "-filter" "-help") #t))))) (inputs - `(("edirect-go-programs" ,edirect-go-programs) + `(("bash" ,bash-minimal) ; for wrap-program + ("edirect-go-programs" ,edirect-go-programs) ("perl-html-parser" ,perl-html-parser) ("perl-encode-locale" ,perl-encode-locale) ("perl-file-listing" ,perl-file-listing) @@ -4952,7 +4960,8 @@ sequencing tag position and orientation.") (find-files bin))) #t))))) (inputs - `(("perl" ,perl) + `(("bash" ,bash-minimal) ; for wrap-program + ("perl" ,perl) ("ruby" ,ruby) ("gawk" ,gawk) ("grep" ,grep) @@ -5485,7 +5494,8 @@ generated using the PacBio Iso-Seq protocol.") (install-file "prank.1" man)) #t))))) (inputs - `(("mafft" ,mafft) + `(("bash" ,bash-minimal) ; for wrap-program + ("mafft" ,mafft) ("exonerate" ,exonerate) ("bppsuite" ,bppsuite))) (home-page "http://wasabiapp.org/software/prank/") @@ -5718,7 +5728,8 @@ partial genes, and identifies translation initiation sites.") ("perl-test-most" ,perl-test-most) ("perl-test-output" ,perl-test-output))) (inputs - `(("perl-array-utils" ,perl-array-utils) + `(("bash" ,bash-minimal) ; for wrap-program + ("perl-array-utils" ,perl-array-utils) ("bioperl" ,bioperl-minimal) ("perl-digest-md5-file" ,perl-digest-md5-file) ("perl-exception-class" ,perl-exception-class) @@ -5871,7 +5882,8 @@ phylogenies.") "rsem-run-prsem-testing-procedure"))) #t))))) (inputs - `(("boost" ,boost) + `(("bash" ,bash-minimal) ; for wrap-program + ("boost" ,boost) ("r-minimal" ,r-minimal) ("perl" ,perl) ("htslib" ,htslib-1.3) @@ -7764,7 +7776,8 @@ data. It also generates basic statistics for your sequences.") (when tests? (invoke "make" "check"))))))) (inputs - `(("boost" ,boost) + `(("bash" ,bash-minimal) ; for wrap-program + ("boost" ,boost) ("htslib" ,htslib) ("python" ,python) ("python-biopython" ,python-biopython) @@ -8035,7 +8048,8 @@ secondary structure and comparative analysis in R.") `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("r-minimal" ,r-minimal) + `(("bash" ,bash-minimal) ; for wrap-program + ("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) ("guile" ,guile-2.2) ("guile-json" ,guile-json-1) @@ -11189,7 +11203,8 @@ conversions, region filtering, FASTA sequence extraction and more.") "unmapped2anchors.py"))) #t))))) (inputs - `(("python2" ,python-2) + `(("bash" ,bash-minimal) ; for wrap-program + ("python2" ,python-2) ("python2-pysam" ,python2-pysam) ("python2-numpy" ,python2-numpy))) (home-page "https://github.com/marvin-jens/find_circ") @@ -12329,7 +12344,8 @@ datasets.") (("awk") (which "gawk"))) #t))))) (inputs - `(("gawk" ,gawk) ;for read_info_histograms.sh + `(("bash" ,bash-minimal) ;for wrap-program + ("gawk" ,gawk) ;for read_info_histograms.sh ("python" ,python-2) ;required for histogram.py ("zlib" ,zlib))) (home-page "https://github.com/rrwick/Filtlong/") @@ -12407,7 +12423,8 @@ choosing which reads pass the filter.") `("PERL5LIB" ":" prefix (,perl5lib)))) (find-files scripts "\\.pl")))))))) (inputs - `(("guile" ,guile-3.0) ; for wrappers + `(("bash" ,bash-minimal) ; for wrap-program + ("guile" ,guile-3.0) ; for other wrappers ("eigen" ,eigen) ("hdf5" ,hdf5) ("htslib" ,htslib) @@ -12707,7 +12724,8 @@ includes a command line tool and an analysis pipeline.") `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("htslib" ,htslib) + `(("bash" ,bash-minimal) ; for wrap-program + ("htslib" ,htslib) ("r-minimal" ,r-minimal) ("r-circlize" ,r-circlize) ("r-genomicalignments" ,r-genomicalignments) @@ -12914,7 +12932,8 @@ downstream analysis.") `("PATH" ":" prefix (,path))))) #t))))) (inputs - `(("infernal" ,infernal) + `(("bash" ,bash-minimal) ; for wrap-program + ("infernal" ,infernal) ("hmmer" ,hmmer))) (propagated-inputs `(("python-biopython" ,python2-biopython) @@ -14172,7 +14191,8 @@ my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir runtests(@test_files); ")))))))) (inputs - `(("bioperl-minimal" ,bioperl-minimal) + `(("bash" ,bash-minimal) ; for wrap-program + ("bioperl-minimal" ,bioperl-minimal) ("perl-bio-db-hts" ,perl-bio-db-hts) ("perl-dbi" ,perl-dbi) ("perl-dbd-mysql" ,perl-dbd-mysql)