From 9a6808e0c00d6acb00b7be4aa573f252fa7d9635 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 11:54:44 +0200 Subject: gnu: tophat: Update to 2.1.1. * gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- .../patches/tophat-build-with-later-seqan.patch | 24 ---------------------- 1 file changed, 24 deletions(-) delete mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch (limited to 'gnu/packages/patches') diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. -This is the relevant part of a patch originally posted here: -https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html - ---- a/src/segment_juncs.cpp -+++ b/src/segment_juncs.cpp -@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl - typedef map MotifMap; - - MotifMap ims; -- -- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -- -+ -+ typedef seqan::ModifiedString< -+ seqan::ModifiedString > >, -+ seqan::ModReverse> ConstDnaStringReverseComplement; -+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -+ - if (talkative) - fprintf(stderr, "Collecting potential splice sites in islands\n"); - -- cgit v1.2.3 From 7321920cd3c9c1d7532024dfcdb958cce54b6368 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:51:31 +0200 Subject: gnu: crossmap: Update to 0.2.9. * gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 25 +---- .../patches/crossmap-allow-system-pysam.patch | 121 --------------------- 3 files changed, 6 insertions(+), 141 deletions(-) delete mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index c167e6753c..c76908f92f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -634,7 +634,6 @@ dist_patch_DATA = \ %D%/packages/patches/cracklib-fix-buffer-overflow.patch \ %D%/packages/patches/crawl-upgrade-saves.patch \ %D%/packages/patches/crda-optional-gcrypt.patch \ - %D%/packages/patches/crossmap-allow-system-pysam.patch \ %D%/packages/patches/clucene-contribs-lib.patch \ %D%/packages/patches/cube-nocheck.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 795b0f208e..6469e9e1a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1894,31 +1894,18 @@ (define-public clustal-omega (define-public crossmap (package (name "crossmap") - (version "0.2.1") + (version "0.2.9") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" - version ".tar.gz")) + (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) - ;; This patch has been sent upstream already and is available - ;; for download from Sourceforge, but it has not been merged. - (patches (search-patches "crossmap-allow-system-pysam.patch")) - (modules '((guix build utils))) - (snippet '(begin - ;; remove bundled copy of pysam - (delete-file-recursively "lib/pysam") - #t)))) + "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-env - (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) + (arguments `(#:python ,python-2)) (inputs - `(("python-numpy" ,python2-numpy) + `(("python-bx-python" ,python2-bx-python) + ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("zlib" ,zlib))) (native-inputs diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch deleted file mode 100644 index 611c4ff74d..0000000000 --- a/gnu/packages/patches/crossmap-allow-system-pysam.patch +++ /dev/null @@ -1,121 +0,0 @@ -This patch modifies the build process such that the bundled copy of pysam does -not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module -can be imported. - -Upstream has agreed to apply the patch in the next maintenance release of -crossmap. The patch has already been uploaded to -http://sourceforge.net/projects/crossmap/files/patch/. - -diff --git a/setup.py b/setup.py ---- a/setup.py 2015-02-26 15:28:49.771189185 +0100 -+++ b/setup.py 2015-02-26 15:55:03.440327752 +0100 -@@ -19,6 +19,15 @@ - except: - have_numpy = False - -+try: -+ import pysam -+ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']: -+ have_pysam = True -+ else: -+ have_pysam = False -+except ImportError: -+ have_pysam = False -+ - if platform.system()=='Windows': - print >> sys.stderr, "Sorry, Windows platform is not supported!" - sys.exit() -@@ -165,49 +174,50 @@ - - - #================= pysam samtools ==================== -- extensions.append(Extension( -- "pysam.csamtools", -- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.ctabix", -- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'), -- ('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.TabProxies", -- tabproxies_sources + os_c_files, -- library_dirs=[], -- include_dirs= include_os, -- libraries=[ "z", ], -- language="c", -- )) -- -- extensions.append(Extension( -- "pysam.cvcf", -- cvcf_sources + os_c_files, -- library_dirs=[], -- include_dirs= ["lib/tabix",] + include_os, -- libraries=[ "z", ], -- language="c", -- )) -+ if not have_pysam: -+ extensions.append(Extension( -+ "pysam.csamtools", -+ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -+ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.ctabix", -+ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'), -+ ('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.TabProxies", -+ tabproxies_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) -+ -+ extensions.append(Extension( -+ "pysam.cvcf", -+ cvcf_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= ["lib/tabix",] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) - - - return extensions -- cgit v1.2.3 From 7a1e62ca67849f9ca19ded4d26c542021db71e38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 14:00:07 +0200 Subject: gnu: delly: Update to 0.7.9. * gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 40 ++++++++-------- .../patches/delly-use-system-libraries.patch | 56 ---------------------- 3 files changed, 20 insertions(+), 77 deletions(-) delete mode 100644 gnu/packages/patches/delly-use-system-libraries.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index c76908f92f..d155b4c613 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -642,7 +642,6 @@ dist_patch_DATA = \ %D%/packages/patches/datamash-arm-tests.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 bc21848367..78debbc873 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2155,42 +2155,42 @@ (define-public deeptools (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (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")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #: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") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((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))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/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 diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3315c2a176..0000000000 --- a/gnu/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- 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) -- cgit v1.2.3 From 9861bcd182b1ba89a93630a2178b170a088f0a6b Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 18 Oct 2018 10:30:35 +0800 Subject: gnu: liblxqt: Update to 0.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0. [source]: Remove patches. [home-page]: Use HTTPS. * gnu/packages/patches/liblxqt-include.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: 宋文武 --- gnu/local.mk | 1 - gnu/packages/lxqt.scm | 39 ++++++++++++++++++++---------- gnu/packages/patches/liblxqt-include.patch | 14 ----------- 3 files changed, 26 insertions(+), 28 deletions(-) delete mode 100644 gnu/packages/patches/liblxqt-include.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index d155b4c613..47883f829e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,7 +885,6 @@ dist_patch_DATA = \ %D%/packages/patches/libjxr-fix-function-signature.patch \ %D%/packages/patches/libjxr-fix-typos.patch \ %D%/packages/patches/libotr-test-auth-fix.patch \ - %D%/packages/patches/liblxqt-include.patch \ %D%/packages/patches/libmad-armv7-thumb-pt1.patch \ %D%/packages/patches/libmad-armv7-thumb-pt2.patch \ %D%/packages/patches/libmad-frame-length.patch \ diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 57dd5b9c2f..c4d0662e99 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -32,7 +32,9 @@ (define-module (gnu packages lxqt) #:use-module (gnu packages glib) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages qt)) + #:use-module (gnu packages polkit) + #:use-module (gnu packages qt) + #:use-module (gnu packages xorg)) (define-public libqtxdg (package @@ -72,29 +74,40 @@ (define-public libqtxdg (define-public liblxqt (package (name "liblxqt") - (version "0.9.0") + (version "0.13.0") (source (origin (method url-fetch) - (uri - (string-append "https://github.com/lxde/" name - "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append + "https://github.com/lxqt/" name "/releases/download/" + version "/" name "-" version ".tar.xz")) (sha256 - (base32 - "0mbl3qc0yfgfsndqrw8vg8k5irsy0pg2wrad8nwv0aphphd4n7rg")) - (patches (search-patches "liblxqt-include.patch")))) + (base32 "0fba0nq5b9fvvmklcikcd4nwhzlp5d6k1q1f80r34kncdzfvj7dl")))) (build-system cmake-build-system) (arguments - `(#:tests? #f)) - (native-inputs `(("pkg-config" ,pkg-config))) + `(#:tests? #f ; no tests + #:configure-flags + ;; TODO: prefetch translations files from 'lxqt-l10n'. + '("-DPULL_TRANSLATIONS=NO") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "CMakeLists.txt" + (("DESTINATION \"\\$\\{POLKITQT-1_POLICY_FILES_INSTALL_DIR\\}") + "DESTINATION \"${CMAKE_INSTALL_PREFIX}/share/polkit-1/actions")) + #t))))) (inputs `(("kwindowsystem" ,kwindowsystem) ("libqtxdg" ,libqtxdg) - ("qtbase" ,qtbase) + ("libxscrnsaver" ,libxscrnsaver) + ("polkit-qt" ,polkit-qt) + ("qtsvg" ,qtsvg) ("qttools" ,qttools) ("qtx11extras" ,qtx11extras))) - (home-page "http://lxqt.org/") + (native-inputs + `(("lxqt-build-tools" ,lxqt-build-tools))) + (home-page "https://lxqt.org/") (synopsis "Core utility library for all LXQt components") (description "liblxqt provides the basic libraries shared by the components of the LXQt desktop environment.") diff --git a/gnu/packages/patches/liblxqt-include.patch b/gnu/packages/patches/liblxqt-include.patch deleted file mode 100644 index 4e8cf04789..0000000000 --- a/gnu/packages/patches/liblxqt-include.patch +++ /dev/null @@ -1,14 +0,0 @@ -Patch to fix build with Qt 5.5, taken from upstream: - https://github.com/lxde/liblxqt/commit/7303ea207de0771d6f450a31ec4a1ce69202869b - -diff -u -r liblxqt-0.9.0.orig/lxqtnotification.h liblxqt-0.9.0/lxqtnotification.h ---- liblxqt-0.9.0.orig/lxqtnotification.h 2015-07-27 22:49:05.365166482 +0200 -+++ liblxqt-0.9.0/lxqtnotification.h 2015-07-27 22:49:36.897606619 +0200 -@@ -25,6 +25,7 @@ - #ifndef LXQTNOTIFICATION_H - #define LXQTNOTIFICATION_H - -+#include - #include - #include "lxqtglobals.h" - -- cgit v1.2.3