From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:59634) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dOA81-0003xF-NA for guix-patches@gnu.org; Thu, 22 Jun 2017 17:59:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dOA7y-0007bX-Ly for guix-patches@gnu.org; Thu, 22 Jun 2017 17:59:05 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:59177) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dOA7y-0007as-HH for guix-patches@gnu.org; Thu, 22 Jun 2017 17:59:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dOA7y-000398-6P for guix-patches@gnu.org; Thu, 22 Jun 2017 17:59:02 -0400 Subject: [bug#27376] [PATCH] gnu: Add kentutils. Resent-Message-ID: From: Kei Kebreau References: <20170615141005.6949-1-ricardo.wurmus@mdc-berlin.de> Date: Thu, 22 Jun 2017 17:57:38 -0400 In-Reply-To: <20170615141005.6949-1-ricardo.wurmus@mdc-berlin.de> (Ricardo Wurmus's message of "Thu, 15 Jun 2017 16:10:05 +0200") Message-ID: <87ziczr8h9.fsf@openmailbox.org> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Ricardo Wurmus Cc: 27376@debbugs.gnu.org --=-=-= Content-Type: text/plain Ricardo Wurmus writes: > * gnu/packages/bioinformatics.scm (kentutils): New variable. > --- > gnu/packages/bioinformatics.scm | 115 ++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 115 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 22a81f160..1f71f80ae 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -50,6 +50,7 @@ > #:use-module (gnu packages cpio) > #:use-module (gnu packages curl) > #:use-module (gnu packages documentation) > + #:use-module (gnu packages databases) > #:use-module (gnu packages datastructures) > #:use-module (gnu packages file) > #:use-module (gnu packages flex) > @@ -84,6 +85,7 @@ > #:use-module (gnu packages readline) > #:use-module (gnu packages ruby) > #:use-module (gnu packages serialization) > + #:use-module (gnu packages shells) > #:use-module (gnu packages statistics) > #:use-module (gnu packages swig) > #:use-module (gnu packages tbb) > @@ -9496,3 +9498,116 @@ correct interaction matrices, identify adn compare the so-called > interaction matrices, and finally, extract structural properties from the > models. TADbit is complemented by TADkit for visualizing 3D models.") > (license license:gpl3+))) > + > +(define-public kentutils > + (package > + (name "kentutils") > + ;; 302.1.0 is out, but the only difference is the inclusion of > + ;; pre-built binaries. > + (version "302.0.0") > + (source > + (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" > + "archive/v" version ".tar.gz")) > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 > + "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) > + (modules '((guix build utils) > + (srfi srfi-26) > + (ice-9 ftw))) > + (snippet > + '(begin > + ;; Only the contents of the specified directories are free > + ;; for all uses, so we remove the rest. "hg/autoSql" and > + ;; "hg/autoXml" are nominally free, but they depend on a > + ;; library that is built from the sources in "hg/lib", > + ;; which is nonfree. > + (let ((free (list "." ".." > + "utils" "lib" "inc" "tagStorm" > + "parasol" "htslib")) > + (directory? (lambda (file) > + (eq? 'directory (stat:type (stat file)))))) > + (for-each (lambda (file) > + (and (directory? file) > + (delete-file-recursively file))) > + (map (cut string-append "src/" <>) > + (scandir "src" > + (lambda (file) > + (not (member file free))))))) > + ;; Only make the utils target, not the userApps target, > + ;; because that requires libraries we won't build. > + (substitute* "Makefile" > + ((" userApps") " utils")) > + ;; Only build libraries that are free. > + (substitute* "src/makefile" > + (("DIRS =.*") "DIRS =\n") > + (("cd jkOwnLib.*") "") > + ((" hgLib") "") > + (("cd hg.*") "")) > + (substitute* "src/utils/makefile" > + ;; These tools depend on "jkhgap.a", which is part of the > + ;; nonfree "src/hg/lib" directory. > + (("raSqlQuery") "") > + (("pslLiftSubrangeBlat") "") > + > + ;; Do not build UCSC tools, which may require nonfree > + ;; components. > + (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) > + #t)))) > + (build-system gnu-build-system) > + (arguments > + `( ;; There is no global test target and the test target for > + ;; individual tools depends on input files that are not > + ;; included. > + #:tests? #f > + #:phases > + (modify-phases %standard-phases > + (add-after 'unpack 'fix-paths > + (lambda _ > + (substitute* "Makefile" > + (("/bin/echo") (which "echo"))) > + #t)) > + (add-after 'unpack 'prepare-samtabix > + (lambda* (#:key inputs #:allow-other-keys) > + (copy-recursively (assoc-ref inputs "samtabix") > + "samtabix") > + #t)) > + (delete 'configure) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let ((bin (string-append (assoc-ref outputs "out") > + "/bin"))) > + (copy-recursively "bin" bin)) > + #t))))) > + (native-inputs > + `(("samtabix" > + ,(origin > + (method git-fetch) > + (uri (git-reference > + (url "http://genome-source.cse.ucsc.edu/samtabix.git") > + (commit "10fd107909c1ac4d679299908be4262a012965ba"))) > + (sha256 > + (base32 > + "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) > + (inputs > + `(("zlib" ,zlib) > + ("tcsh" ,tcsh) > + ("perl" ,perl) > + ("libpng" ,libpng) > + ("mysql" ,mysql) > + ("openssl" ,openssl))) > + (home-page "http://genome.cse.ucsc.edu/index.html") > + (synopsis "Assorted bioinformatics utilities") > + (description "This package provides the kentUtils, a selection of > +bioinformatics utilities used in combination with the UCSC genome > +browser.") > + ;; Only a subset of the sources are released under a non-copyleft > + ;; free software license. All other sources are removed in a > + ;; snippet. See this bug report for an explanation of how the > + ;; license statements apply: > + ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 > + (license (license:non-copyleft > + "http://genome.ucsc.edu/license/" > + "The contents of this package are free for all uses.")))) 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