From unknown Fri Jun 13 10:22:49 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30985] [PATCH] gnu: Add delly. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Mar 2018 13:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 30985 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30985@debbugs.gnu.org X-Debbugs-Original-To: guix-patches Received: via spool by submit@debbugs.gnu.org id=B.15223285695200 (code B ref -1); Thu, 29 Mar 2018 13:03:02 +0000 Received: (at submit) by debbugs.gnu.org; 29 Mar 2018 13:02:49 +0000 Received: from localhost ([127.0.0.1]:58137 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1XCX-0001Li-Ul for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:49 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39826) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1XCT-0001LN-KQ for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1XCK-0008L2-3I for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:36 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:60093) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1f1XCK-0008Kx-0U for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:32 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58973) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1XC9-0005wS-PQ for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1XC6-0008Ek-5z for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:21 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:42227) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1XC6-0008Eg-0M for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:18 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:24842 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1f1XC5-00072n-Cj for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:17 -0400 User-agent: mu4e 1.0; emacs 25.3.1 From: Roel Janssen Date: Thu, 29 Mar 2018 15:02:12 +0200 Message-ID: <87zi2r3ui3.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) --=-=-= Content-Type: text/plain Dear Guix, I'd like to add Delly. Note that there's a newer version (0.7.8) out. We extensively tested 0.7.7 in our research lab. Building 0.7.8 failed because the patch for unbundling dependencies no longer applies to this new version. So I'd like to add 0.7.7 first, and do more testing/patching on 0.7.8 before we update it in Guix. Thanks for your time! Kind regards, Roel Janssen --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-delly.patch >From b333dd0f027e8dfdcd67bc96ab94f6fc79cf0854 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Mar 2018 14:58:15 +0200 Subject: [PATCH] gnu: Add delly. * gnu/packages/bioinformatics.scm (delly): New variable. * gnu/packages/patches/delly-use-system-libraries.patch: New file. * gnu/local.mk: Include delly-use-system-libraries.patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++ .../patches/delly-use-system-libraries.patch | 56 ++++++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 gnu/packages/patches/delly-use-system-libraries.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0575a2fe3..2705fb37a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -621,6 +621,7 @@ dist_patch_DATA = \ %D%/packages/patches/cyrus-sasl-CVE-2013-4122.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ + %D%/packages/patches/delly-use-system-libraries.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ %D%/packages/patches/diffutils-gets-undeclared.patch \ %D%/packages/patches/diffutils-getopt.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b16ee2b60..76349d426 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2030,6 +2030,60 @@ normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.") (license license:gpl3+))) +(define-public delly + (package + (name "delly") + (version "0.7.7") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/tobiasrausch/delly/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) + (patches + (list + (search-patch "delly-use-system-libraries.patch"))))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda _ + (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) + (templates (string-append (assoc-ref %outputs "out") + "/share/delly/templates"))) + (mkdir-p bin) + (mkdir-p templates) + (copy-recursively "excludeTemplates" templates) + (install-file "src/cov" bin) + (install-file "src/delly" bin) + (install-file "src/dpe" bin))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("bzip2" ,bzip2))) + (native-inputs + `(("python" ,python-2))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("bzip2" ,bzip2))) + (home-page "https://github.com/tobiasrausch/delly") + (synopsis "Integrated structural variant prediction method") + (description "Delly is an integrated structural variant prediction method +that can discover and genotype deletions, tandem duplications, inversions and +translocations at single-nucleotide resolution in short-read massively parallel +sequencing data. It uses paired-ends and split-reads to sensitively and +accurately delineate genomic rearrangements throughout the genome.") + (license license:gpl3+))) + (define-public diamond (package (name "diamond") diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch new file mode 100644 index 000000000..3315c2a17 --- /dev/null +++ b/gnu/packages/patches/delly-use-system-libraries.patch @@ -0,0 +1,56 @@ +--- a/Makefile 2017-04-09 12:48:15.000000000 +0200 ++++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 +@@ -9,8 +9,8 @@ + + # Flags + CXX=g++ +-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing +-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time ++CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing ++LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time + + # Additional flags for release/debug + ifeq (${PARALLEL}, 1) +@@ -23,7 +23,7 @@ + ifeq (${STATIC}, 1) + LDFLAGS += -static -static-libgcc -pthread -lhts -lz + else +- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib ++ LDFLAGS += -lhts -lz + endif + ifeq (${DEBUG}, 1) + CXXFLAGS += -g -O0 -fno-inline -DDEBUG +@@ -41,29 +41,17 @@ + DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) + + # Targets +-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe ++TARGETS = src/delly src/cov src/dpe + + all: $(TARGETS) + +-.htslib: $(HTSLIBSOURCES) +- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib +- +-.bcftools: $(HTSLIBSOURCES) +- cd src/bcftools && make && cd ../../ && touch .bcftools +- +-.boost: $(BOOSTSOURCES) +- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost +- +-src/delly: .htslib .bcftools .boost $(DELLYSOURCES) +- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) +- +-src/cov: .htslib .bcftools .boost $(DELLYSOURCES) ++src/cov: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + +-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) ++src/dpe: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + + clean: + cd src/htslib && make clean + cd src/modular-boost && ./b2 --clean-all +- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools ++ rm -f $(TARGETS) $(TARGETS:=.o) -- 2.16.2 --=-=-=-- From unknown Fri Jun 13 10:22:49 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Roel Janssen Subject: bug#30985: closed (Re: [bug#30985] [PATCH] gnu: Add delly.) Message-ID: References: <20180330145116.GB21544@jasmine.lan> <87zi2r3ui3.fsf@gnu.org> X-Gnu-PR-Message: they-closed 30985 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 30985@debbugs.gnu.org Date: Fri, 30 Mar 2018 14:52:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1522421522-3969-1" This is a multi-part message in MIME format... ------------=_1522421522-3969-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #30985: [PATCH] gnu: Add delly. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 30985@debbugs.gnu.org. --=20 30985: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D30985 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1522421522-3969-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 30985-done) by debbugs.gnu.org; 30 Mar 2018 14:51:21 +0000 Received: from localhost ([127.0.0.1]:60343 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1vNB-000118-HS for submit@debbugs.gnu.org; Fri, 30 Mar 2018 10:51:21 -0400 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:45103) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1vN8-00010z-Ja for 30985-done@debbugs.gnu.org; Fri, 30 Mar 2018 10:51:18 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id 6D0D320D76; Fri, 30 Mar 2018 10:51:18 -0400 (EDT) Received: from mailfrontend2 ([10.202.2.163]) by compute4.internal (MEProxy); Fri, 30 Mar 2018 10:51:18 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=cc:content-type:date:from:in-reply-to:message-id:mime-version :references:subject:to:x-me-sender:x-me-sender:x-sasl-enc; s= mesmtp; bh=6oVTnC/MWeZi5Csr3m40ZS/GqDDCWOWGAfDzPHVlD7g=; b=nAd64 vG+gzXoCGVNqhTC/5d7geOU0lv81VqOxYt+k6T8xTyrB6KWhEk6l+MlCsxifjMfa kSkU0O3iolzpWVVuGenyEUOnyCuVgar//Xk70aoJrqd+/NZxrAlD4Oa0ca7rbSiW 50q8hmFZtthxEJ4wpf6+Qw2ZbvYjSpl2BjZiLs= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-sender :x-me-sender:x-sasl-enc; s=fm2; bh=6oVTnC/MWeZi5Csr3m40ZS/GqDDCW OWGAfDzPHVlD7g=; b=DXbn1Ag1SACUT5y5yda1BzrS5Z4My0cat+QTmmbSaj3vB sJLE1dbDgpsWgTRHoyL+jRqQ03mR/0a4dxIfALHK/CunfZjD4fx5m0UEZarfnmLs 4Pb8O1f6g/yEmZ5Xa7ps0slcMG2Slz58c+CZkQ2P1XTV2SaRW0m4tYVKcaKwFnjN bB1D4OQg7h9f1Ex3T3ls1vavkhCc/sqiiUUdHoIZiztOpyYpZ1nR1/dn2JNumug5 fr2HAwjveB6hcScdHClN81YA27x9eWaGZDPLkKAIQsNwl1/z/003w1ZEA+c486n4 ygk/K4wwRFkOfnu3IOcrbmQ5hIwdTStzz7bJwZHmg== X-ME-Sender: Received: from localhost (unknown [172.58.201.190]) by mail.messagingengine.com (Postfix) with ESMTPA id 05A2710269; Fri, 30 Mar 2018 10:51:17 -0400 (EDT) Date: Fri, 30 Mar 2018 10:51:16 -0400 From: Leo Famulari To: Roel Janssen Subject: Re: [bug#30985] [PATCH] gnu: Add delly. Message-ID: <20180330145116.GB21544@jasmine.lan> References: <87zi2r3ui3.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="3lcZGd9BuhuYXNfi" Content-Disposition: inline In-Reply-To: <87zi2r3ui3.fsf@gnu.org> User-Agent: Mutt/1.9.3 (2018-01-21) X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 30985-done Cc: 30985-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) --3lcZGd9BuhuYXNfi Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Mar 29, 2018 at 03:02:12PM +0200, Roel Janssen wrote: > Dear Guix, >=20 > I'd like to add Delly. Note that there's a newer version (0.7.8) out. > We extensively tested 0.7.7 in our research lab. Building 0.7.8 failed > because the patch for unbundling dependencies no longer applies to this > new version. >=20 > So I'd like to add 0.7.7 first, and do more testing/patching on 0.7.8 > before we update it in Guix. Okay! > From b333dd0f027e8dfdcd67bc96ab94f6fc79cf0854 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Thu, 29 Mar 2018 14:58:15 +0200 > Subject: [PATCH] gnu: Add delly. >=20 > * gnu/packages/bioinformatics.scm (delly): New variable. > * gnu/packages/patches/delly-use-system-libraries.patch: New file. > * gnu/local.mk: Include delly-use-system-libraries.patch. Pushed as fdc306879b388b08be63ead6209473c184daa1e0 with these changes: > + (patches > + (list > + (search-patch "delly-use-system-libraries.patch"))))) I changed this to use search-patches... > + (inputs > + `(("boost" ,boost) > + ("htslib" ,htslib) > + ("zlib" ,zlib) > + ("bzip2" ,bzip2))) > + (native-inputs > + `(("python" ,python-2))) > + (inputs > + `(("boost" ,boost) > + ("htslib" ,htslib) > + ("zlib" ,zlib) > + ("bzip2" ,bzip2))) =2E.. and removed the extra part. --3lcZGd9BuhuYXNfi Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAlq+TuQACgkQJkb6MLrK fwjRNRAAx/ODjV+b2OAJp/eneDFvn3ghZIGQ5WEgBGXjVE0KbkEBlnVPdV8RHaB4 Wls+jvfyJWliNv/mzFdMZmkH05tCA5VpGcjHm6IisQFUEtyP8/o09DSdqpCE+VJx 0R6ZoVfDOeIbV05myV2jZoo2hsFv1/wL1P/F5X5MXOClMbSqMauGMqiQJasT/VJa p5ViCSkGKg+jTHwP/yrvzbClKOshR62KIx8FxKFGyc3y/jnFh5U+uYDmm7LfZ1h6 iLio/MDChQh2YNjqwnGVlpU8F6j/br+XaREGnDeDyaNcvyLdW8RUSZsSQ/C97y19 hY7hxXUREnZeqTfatlYm2nLMU6vwWdCo9jLp2N41Wgs0rTU+K6C2bBT4sNv1Wksz Lfl2T9/LNLZLxbqp1qW+KaazrCdiOsRwx3hwnvG0fqTLL8D2Q90Ovv+/QZsNOcUW 260ZIBv5rzIrNQy0S0868YhdNPwdVAZYRS0EEtWs1cNZ/qQNiDGmxs6GtS6zBrro OPrHpQ3PU+GMqx1ZbgunFfMaRp+bTTDP25OjVcghukSmVAK0usJFZ3PXy/0pZXaK 9mD4HCQxiz1WyrIstNMXUybj3fGw5wGv1mvTRC3Dlnj/+RBKC8rIrQ9rf/sTMzXz E0T/yumwa2GzCBybK48usctSIhikRmej1Y/V3kQzRbrsTkl/esY= =1Vqj -----END PGP SIGNATURE----- --3lcZGd9BuhuYXNfi-- ------------=_1522421522-3969-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 29 Mar 2018 13:02:49 +0000 Received: from localhost ([127.0.0.1]:58137 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1XCX-0001Li-Ul for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:49 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39826) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1XCT-0001LN-KQ for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1XCK-0008L2-3I for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:36 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:60093) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1f1XCK-0008Kx-0U for submit@debbugs.gnu.org; Thu, 29 Mar 2018 09:02:32 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58973) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1XC9-0005wS-PQ for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1XC6-0008Ek-5z for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:21 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:42227) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1XC6-0008Eg-0M for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:18 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:24842 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1f1XC5-00072n-Cj for guix-patches@gnu.org; Thu, 29 Mar 2018 09:02:17 -0400 User-agent: mu4e 1.0; emacs 25.3.1 From: Roel Janssen To: guix-patches Subject: [PATCH] gnu: Add delly. Date: Thu, 29 Mar 2018 15:02:12 +0200 Message-ID: <87zi2r3ui3.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) --=-=-= Content-Type: text/plain Dear Guix, I'd like to add Delly. Note that there's a newer version (0.7.8) out. We extensively tested 0.7.7 in our research lab. Building 0.7.8 failed because the patch for unbundling dependencies no longer applies to this new version. So I'd like to add 0.7.7 first, and do more testing/patching on 0.7.8 before we update it in Guix. Thanks for your time! Kind regards, Roel Janssen --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-delly.patch >From b333dd0f027e8dfdcd67bc96ab94f6fc79cf0854 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Mar 2018 14:58:15 +0200 Subject: [PATCH] gnu: Add delly. * gnu/packages/bioinformatics.scm (delly): New variable. * gnu/packages/patches/delly-use-system-libraries.patch: New file. * gnu/local.mk: Include delly-use-system-libraries.patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++ .../patches/delly-use-system-libraries.patch | 56 ++++++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 gnu/packages/patches/delly-use-system-libraries.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0575a2fe3..2705fb37a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -621,6 +621,7 @@ dist_patch_DATA = \ %D%/packages/patches/cyrus-sasl-CVE-2013-4122.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ + %D%/packages/patches/delly-use-system-libraries.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ %D%/packages/patches/diffutils-gets-undeclared.patch \ %D%/packages/patches/diffutils-getopt.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b16ee2b60..76349d426 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2030,6 +2030,60 @@ normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.") (license license:gpl3+))) +(define-public delly + (package + (name "delly") + (version "0.7.7") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/tobiasrausch/delly/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) + (patches + (list + (search-patch "delly-use-system-libraries.patch"))))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda _ + (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) + (templates (string-append (assoc-ref %outputs "out") + "/share/delly/templates"))) + (mkdir-p bin) + (mkdir-p templates) + (copy-recursively "excludeTemplates" templates) + (install-file "src/cov" bin) + (install-file "src/delly" bin) + (install-file "src/dpe" bin))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("bzip2" ,bzip2))) + (native-inputs + `(("python" ,python-2))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("bzip2" ,bzip2))) + (home-page "https://github.com/tobiasrausch/delly") + (synopsis "Integrated structural variant prediction method") + (description "Delly is an integrated structural variant prediction method +that can discover and genotype deletions, tandem duplications, inversions and +translocations at single-nucleotide resolution in short-read massively parallel +sequencing data. It uses paired-ends and split-reads to sensitively and +accurately delineate genomic rearrangements throughout the genome.") + (license license:gpl3+))) + (define-public diamond (package (name "diamond") diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch new file mode 100644 index 000000000..3315c2a17 --- /dev/null +++ b/gnu/packages/patches/delly-use-system-libraries.patch @@ -0,0 +1,56 @@ +--- a/Makefile 2017-04-09 12:48:15.000000000 +0200 ++++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 +@@ -9,8 +9,8 @@ + + # Flags + CXX=g++ +-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing +-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time ++CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing ++LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time + + # Additional flags for release/debug + ifeq (${PARALLEL}, 1) +@@ -23,7 +23,7 @@ + ifeq (${STATIC}, 1) + LDFLAGS += -static -static-libgcc -pthread -lhts -lz + else +- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib ++ LDFLAGS += -lhts -lz + endif + ifeq (${DEBUG}, 1) + CXXFLAGS += -g -O0 -fno-inline -DDEBUG +@@ -41,29 +41,17 @@ + DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) + + # Targets +-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe ++TARGETS = src/delly src/cov src/dpe + + all: $(TARGETS) + +-.htslib: $(HTSLIBSOURCES) +- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib +- +-.bcftools: $(HTSLIBSOURCES) +- cd src/bcftools && make && cd ../../ && touch .bcftools +- +-.boost: $(BOOSTSOURCES) +- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost +- +-src/delly: .htslib .bcftools .boost $(DELLYSOURCES) +- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) +- +-src/cov: .htslib .bcftools .boost $(DELLYSOURCES) ++src/cov: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + +-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) ++src/dpe: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + + clean: + cd src/htslib && make clean + cd src/modular-boost && ./b2 --clean-all +- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools ++ rm -f $(TARGETS) $(TARGETS:=.o) -- 2.16.2 --=-=-=-- ------------=_1522421522-3969-1-- From unknown Fri Jun 13 10:22:49 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30985] [PATCH] gnu: Add delly. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 30 Mar 2018 21:46:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 30985 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Leo Famulari Cc: 30985-done@debbugs.gnu.org Received: via spool by 30985-done@debbugs.gnu.org id=D30985.152244635614924 (code D ref 30985); Fri, 30 Mar 2018 21:46:01 +0000 Received: (at 30985-done) by debbugs.gnu.org; 30 Mar 2018 21:45:56 +0000 Received: from localhost ([127.0.0.1]:60498 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f21qN-0003se-Qe for submit@debbugs.gnu.org; Fri, 30 Mar 2018 17:45:56 -0400 Received: from eggs.gnu.org ([208.118.235.92]:50305) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f21qK-0003sO-3P for 30985-done@debbugs.gnu.org; Fri, 30 Mar 2018 17:45:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f21qB-0000Hl-Qa for 30985-done@debbugs.gnu.org; Fri, 30 Mar 2018 17:45:46 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:34769) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f21qB-0000Hf-NU; Fri, 30 Mar 2018 17:45:43 -0400 Received: from [89.205.224.22] (port=4485 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1f21qB-00079U-5x; Fri, 30 Mar 2018 17:45:43 -0400 References: <87zi2r3ui3.fsf@gnu.org> <20180330145116.GB21544@jasmine.lan> User-agent: mu4e 1.0; emacs 25.3.1 From: Roel Janssen In-reply-to: <20180330145116.GB21544@jasmine.lan> Date: Fri, 30 Mar 2018 23:45:16 +0200 Message-ID: <87605d5jbn.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Leo Famulari writes: > On Thu, Mar 29, 2018 at 03:02:12PM +0200, Roel Janssen wrote: >> Dear Guix, >> >> I'd like to add Delly. Note that there's a newer version (0.7.8) out. >> We extensively tested 0.7.7 in our research lab. Building 0.7.8 failed >> because the patch for unbundling dependencies no longer applies to this >> new version. >> >> So I'd like to add 0.7.7 first, and do more testing/patching on 0.7.8 >> before we update it in Guix. > > Okay! > >> From b333dd0f027e8dfdcd67bc96ab94f6fc79cf0854 Mon Sep 17 00:00:00 2001 >> From: Roel Janssen >> Date: Thu, 29 Mar 2018 14:58:15 +0200 >> Subject: [PATCH] gnu: Add delly. >> >> * gnu/packages/bioinformatics.scm (delly): New variable. >> * gnu/packages/patches/delly-use-system-libraries.patch: New file. >> * gnu/local.mk: Include delly-use-system-libraries.patch. > > Pushed as fdc306879b388b08be63ead6209473c184daa1e0 with these changes: > >> + (patches >> + (list >> + (search-patch "delly-use-system-libraries.patch"))))) > > I changed this to use search-patches... > >> + (inputs >> + `(("boost" ,boost) >> + ("htslib" ,htslib) >> + ("zlib" ,zlib) >> + ("bzip2" ,bzip2))) >> + (native-inputs >> + `(("python" ,python-2))) >> + (inputs >> + `(("boost" ,boost) >> + ("htslib" ,htslib) >> + ("zlib" ,zlib) >> + ("bzip2" ,bzip2))) > > ... and removed the extra part. Oops.. Thanks for fixing this and pushing! Kind regards, Roel Janssen