From 9a40b8d9b2876867faf1eb593cc347ebf02df89a Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 17 Mar 2018 12:19:24 +1000 Subject: gnu: diamond: Update to 0.9.19. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1da25805..909167ffb1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2033,7 +2033,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.18") + (version "0.9.19") (source (origin (method url-fetch) (uri (string-append @@ -2042,7 +2042,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f")))) + "0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit v1.2.3 From c7a8aa131dc02b0020309b0bcc0c92d3811f8c8b Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 17 Mar 2018 12:17:09 +1000 Subject: gnu: mafft: Update to 7.394. * gnu/packages/bioinformatics.scm (mafft): Update to 7.394. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 909167ffb1..cf36b3642f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3689,7 +3689,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.313") + (version "7.394") (source (origin (method url-fetch) (uri (string-append @@ -3698,7 +3698,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0r83qmg2if8mi6jyx3xdf8ar2gcxl7r9nmj98jr7lxym97v61a2k")))) + "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me -- cgit v1.2.3 From f38ac742e6f542110cf838646a35c325201def51 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 4 Mar 2018 10:32:56 +1000 Subject: gnu: mash: Update to 2.0. * gnu/packages/bioinformatics.scm (mash): Update to 2.0. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cf36b3642f..af515c026e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3775,7 +3775,7 @@ sequences).") (define-public mash (package (name "mash") - (version "1.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (string-append @@ -3784,7 +3784,7 @@ sequences).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) + "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) (modules '((guix build utils))) (snippet ;; Delete bundled kseq. @@ -3802,7 +3802,9 @@ sequences).") (modify-phases %standard-phases (add-after 'unpack 'fix-includes (lambda _ - (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") + (substitute* '("src/mash/Sketch.cpp" + "src/mash/CommandFind.cpp" + "src/mash/CommandScreen.cpp") (("^#include \"kseq\\.h\"") "#include \"htslib/kseq.h\"")) #t)) -- cgit v1.2.3 From fdc306879b388b08be63ead6209473c184daa1e0 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Mar 2018 14:58:15 +0200 Subject: 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. Signed-off-by: Leo Famulari --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 47 ++++++++++++++++++ .../patches/delly-use-system-libraries.patch | 56 ++++++++++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 gnu/packages/patches/delly-use-system-libraries.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 0575a2fe32..2705fb37a5 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 af515c026e..66d5bd3707 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2030,6 +2030,53 @@ 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 (search-patches "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))))))) + (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 0000000000..3315c2a176 --- /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) -- cgit v1.2.3 From 262ee8eae27d14b1469b41d07c6a2cbfc7f4905d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 6 Apr 2018 17:06:52 +0200 Subject: gnu: htslib-for-sambamba: Fix build. * gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not inherit htslib arguments. --- gnu/packages/bioinformatics.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 66d5bd3707..88aa48cd9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10987,12 +10987,10 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) (arguments - (substitute-keyword-arguments (package-arguments htslib) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vif")))))))) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) -- cgit v1.2.3 From 482959ffa4601eff181688ec0e7ecaf68fe799a0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 6 Apr 2018 17:07:44 +0200 Subject: gnu: sambamba: Update to 0.6.7-10-g223fa20. * gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git. [arguments]: Disable parallel build; rename build phase "place-biod" to "place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase "unbundle-prerequisites". [native-inputs]: Add python2-minimal; update biod sources; add undead sources. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++------------ 1 file changed, 36 insertions(+), 15 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 88aa48cd9e..0e9e6b13fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10999,34 +10999,41 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (define-public sambamba (package (name "sambamba") - (version "0.6.5") + (version "0.6.7-10-g223fa20") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/lomereiter/sambamba/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lomereiter/sambamba.git") + (commit (string-append "v" version)))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy")))) + "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there is no test target - #:make-flags - '("D_COMPILER=ldc2" - ;; Override "--compiler" flag only. - "D_FLAGS=--compiler=ldc2 -IBioD -g -d" - "sambamba-ldmd2-64") + `(#:tests? #f ; there is no test target + #:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (delete 'configure) - (add-after 'unpack 'place-biod + (add-after 'unpack 'fix-ldc-version + (lambda _ + (substitute* "gen_ldc_version_info.py" + (("/usr/bin/env.*") (which "python"))) + (substitute* "Makefile" + (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + #t)) + (add-after 'unpack 'place-biod-and-undead (lambda* (#:key inputs #:allow-other-keys) (copy-recursively (assoc-ref inputs "biod") "BioD") + (copy-recursively (assoc-ref inputs "undead") "undeaD") #t)) (add-after 'unpack 'unbundle-prerequisites (lambda _ (substitute* "Makefile" + (("htslib/libhts.a lz4/lib/liblz4.a") + "-L-lhts -L-llz4") ((" htslib-static lz4-static") "")) #t)) (replace 'install @@ -11039,8 +11046,9 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) + ("python" ,python2-minimal) ("biod" - ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")) + ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) (origin (method git-fetch) (uri (git-reference @@ -11051,7 +11059,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") "-checkout")) (sha256 (base32 - "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))) + "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) + ("undead" + ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dlang/undeaD.git") + (commit commit))) + (file-name (string-append "undead-" + (string-take commit 9) + "-checkout")) + (sha256 + (base32 + "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) -- cgit v1.2.3