From d6e63cf31cc113e310cd0e5dda9ac4f73a5caeae Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 14 Jul 2017 18:54:03 +1000 Subject: gnu: bowtie: Update to 2.3.2. * gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2. [inputs]: Add zlib. --- gnu/packages/bioinformatics.scm | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82cd1e420d..a9f6259897 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1195,7 +1195,7 @@ errors at the end of reads.") (define-public bowtie (package (name "bowtie") - (version "2.2.9") + (version "2.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" @@ -1203,7 +1203,7 @@ errors at the end of reads.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1vp5db8i7is57iwjybcdg18f5ivyzlj5g1ix1nlvxainzivhz55g")) + "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) (modules '((guix build utils))) (snippet '(substitute* "Makefile" @@ -1211,12 +1211,14 @@ errors at the end of reads.") (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) (build-system gnu-build-system) - (inputs `(("perl" ,perl) - ("perl-clone" ,perl-clone) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-simple" ,perl-test-simple) - ("python" ,python-2) - ("tbb" ,tbb))) + (inputs + `(("perl" ,perl) + ("perl-clone" ,perl-clone) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-simple" ,perl-test-simple) + ("python" ,python-2) + ("tbb" ,tbb) + ("zlib" ,zlib))) (arguments '(#:make-flags (list "allall" -- cgit v1.2.3 From 06e372360eed08a1cbbb2081a591fbfa4785a2f2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 14 Jul 2017 19:23:37 +1000 Subject: gnu: bowtie: Use 'modify-phases'. * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases' syntax. --- gnu/packages/bioinformatics.scm | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a9f6259897..b5ee9cc125 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1225,16 +1225,14 @@ errors at the end of reads.") "WITH_TBB=1" (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases - (alist-delete - 'configure - (alist-replace - 'check - (lambda* (#:key outputs #:allow-other-keys) - (system* "perl" - "scripts/test/simple_tests.pl" - "--bowtie2=./bowtie2" - "--bowtie2-build=./bowtie2-build")) - %standard-phases)))) + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + (lambda* (#:key outputs #:allow-other-keys) + (zero? (system* "perl" + "scripts/test/simple_tests.pl" + "--bowtie2=./bowtie2" + "--bowtie2-build=./bowtie2-build"))))))) (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description -- cgit v1.2.3 From 2805f9b2a026a34d3e1069e86293ab3e18cadd9f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 18 Jul 2017 08:58:59 +0300 Subject: gnu: raxml: Limit to x86_64 and i686 only. * gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5ee9cc125..9acd5454b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4320,6 +4320,8 @@ extremely diverse sets of genomes.") (description "RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.") + ;; The source includes x86 specific code + (supported-systems '("x86_64-linux" "i686-linux")) (license license:gpl2+))) (define-public rsem -- cgit v1.2.3 From 2324541bd0b2febda96eb0004ac3a7bef1fe9d56 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 19 Jul 2017 14:36:52 +0300 Subject: gnu: sortmerna: Limit support to x86_64 and i686 only. * gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9acd5454b3..734bf31670 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5318,6 +5318,8 @@ and operational taxonomic unit (OTU) picking of next generation sequencing (NGS) reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.") + ;; The source includes x86 specific code + (supported-systems '("x86_64-linux" "i686-linux")) (license license:lgpl3))) (define-public star -- cgit v1.2.3 From fd4085793818ab2aea28dfeeb2728f6f02416c4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jul 2017 14:38:37 +0200 Subject: gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash. * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Update hash because the tarball changed in place. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 734bf31670..1caddb9eed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7563,7 +7563,7 @@ Stephens (1990).") version ".tar.gz")) (sha256 (base32 - "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) + "0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) -- cgit v1.2.3 From a35a1e9c13a03dddc38e75c2393fe123405ce88e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 22 Jul 2017 17:22:07 +0200 Subject: gnu: r-genomicranges: Update to 1.28.4. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4. --- 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 1caddb9eed..b5bf562d06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6784,13 +6784,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.28.0") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "10x9zx0b7j05d1j6p0xs4q4f4wzbhf3rq64wzi9cgv7f44q43a5n")))) + "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 3a4b0b126bf602f44807638d80296ff2d215a924 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 22 Jul 2017 17:31:19 +0200 Subject: gnu: r-s4vectors: Update to 0.14.3. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3. --- 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 b5bf562d06..16339f9d6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6532,13 +6532,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.14.0") + (version "0.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0ywwrs4d752xfk0p0w122kvi0xvp6nmxnyynchbsa8zciqymhgv8")))) + "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From c842d425933d0b7d6c5e88bb5fd52c3008b8951d Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 6 Apr 2017 22:27:23 +1000 Subject: gnu: samtools: Use "modify-phases" syntax. * gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++---------------------- 1 file changed, 19 insertions(+), 22 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 16339f9d6e..7669b4c3f0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4533,29 +4533,26 @@ to the user's query of interest.") #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) #:configure-flags (list "--with-ncurses") #:phases - (alist-cons-after - 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") (which "bash"))) - #t) - (alist-cons-after - 'install 'install-library - (lambda* (#:key outputs #:allow-other-keys) - (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (install-file "libbam.a" lib) + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") (which "bash"))) #t)) - (alist-cons-after - 'install 'install-headers - (lambda* (#:key outputs #:allow-other-keys) - (let ((include (string-append (assoc-ref outputs "out") - "/include/samtools/"))) - (for-each (lambda (file) - (install-file file include)) - (scandir "." (lambda (name) (string-match "\\.h$" name)))) - #t)) - %standard-phases))))) + (add-after 'install 'install-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (install-file "libbam.a" lib) + #t))) + (add-after 'install 'install-headers + (lambda* (#:key outputs #:allow-other-keys) + (let ((include (string-append (assoc-ref outputs "out") + "/include/samtools/"))) + (for-each (lambda (file) + (install-file file include)) + (scandir "." (lambda (name) (string-match "\\.h$" name)))) + #t)))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("ncurses" ,ncurses) ("perl" ,perl) -- cgit v1.2.3 From a9e4a1e641c3d24ce2aab65546dcac1fd9c37e47 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 6 Apr 2017 22:57:31 +1000 Subject: gnu: htslib: Update to 1.4.1. * gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl. --- 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 7669b4c3f0..97a58a5371 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3051,7 +3051,7 @@ manipulating HTS data.") (define-public htslib (package (name "htslib") - (version "1.3.1") + (version "1.4.1") (source (origin (method url-fetch) (uri (string-append @@ -3059,7 +3059,7 @@ manipulating HTS data.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))) + "1crkk79kgxcmrkmh5f58c4k93w4rz6lp97sfsq3s6556zxcxvll5")))) (build-system gnu-build-system) (arguments `(#:phases @@ -3071,7 +3071,9 @@ manipulating HTS data.") (("/bin/bash") (which "bash"))) #t))))) (inputs - `(("zlib" ,zlib))) + `(("openssl" ,openssl) + ("curl" ,curl) + ("zlib" ,zlib))) (native-inputs `(("perl" ,perl))) (home-page "http://www.htslib.org") -- cgit v1.2.3 From 4ab1644049ad2d1cf7a997dfa910a4d7d646e49f Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 6 Apr 2017 22:51:26 +1000 Subject: gnu: samtools: Update to 1.4.1. * gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib. --- gnu/packages/bioinformatics.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97a58a5371..f5122a1802 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4516,7 +4516,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.3.1") + (version "1.4.1") (source (origin (method url-fetch) @@ -4525,7 +4525,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc")))) + "0vzxjm5vkgvzynl7cssm1l560rqs2amdaib1x8sp2ch9b7bxx9xx")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -4533,7 +4533,7 @@ to the user's query of interest.") (guix build gnu-build-system) (guix build utils)) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) - #:configure-flags (list "--with-ncurses") + #:configure-flags (list "--with-ncurses" "--with-htslib=system") #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-tests @@ -4556,10 +4556,12 @@ to the user's query of interest.") (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)))))) (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))) + (inputs + `(("htslib" ,htslib) + ("ncurses" ,ncurses) + ("perl" ,perl) + ("python" ,python) + ("zlib" ,zlib))) (home-page "http://samtools.sourceforge.net") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (description -- cgit v1.2.3 From 98593f9f51c8f6e3c2208d8443fdf08cf4d633bb Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 7 Apr 2017 19:21:28 +1000 Subject: gnu: bcftools: Update to 1.4.1. * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 20 +++++--------- gnu/packages/patches/bcftools-fix-makefile.patch | 33 ++++++++++++++++++++++++ 3 files changed, 41 insertions(+), 13 deletions(-) create mode 100644 gnu/packages/patches/bcftools-fix-makefile.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 8d3916e26d..3397216e15 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -522,6 +522,7 @@ dist_patch_DATA = \ %D%/packages/patches/awesome-reproducible-png.patch \ %D%/packages/patches/azr3.patch \ %D%/packages/patches/bash-completion-directories.patch \ + %D%/packages/patches/bcftools-fix-makefile.patch \ %D%/packages/patches/binutils-ld-new-dtags.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/binutils-mips-bash-bug.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5122a1802..87da4aed15 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -300,7 +300,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.3.1") + (version "1.4.1") (source (origin (method url-fetch) (uri (string-append @@ -308,11 +308,12 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj")) + "024xv59bzv148b6w3das4jmldf7rywsf8y1fbqznap008qc8gl6p")) + (patches (search-patches "bcftools-fix-makefile.patch")) (modules '((guix build utils))) (snippet ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.3.1")))) + '(delete-file-recursively "htslib-1.4.1")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -321,19 +322,12 @@ BAM files.") "USE_GPL=1" (string-append "prefix=" (assoc-ref %outputs "out")) (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") - (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a") + (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") - (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")) + (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix") + (string-append "PACKAGE_VERSION=" ,version)) #:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-Makefile - (lambda _ - (substitute* "Makefile" - ;; Do not attempt to build htslib. - (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "") - ;; Link against GSL cblas. - (("-lcblas") "-lgslcblas")) - #t)) (delete 'configure) (add-before 'check 'patch-tests (lambda _ diff --git a/gnu/packages/patches/bcftools-fix-makefile.patch b/gnu/packages/patches/bcftools-fix-makefile.patch new file mode 100644 index 0000000000..614f5fd6bd --- /dev/null +++ b/gnu/packages/patches/bcftools-fix-makefile.patch @@ -0,0 +1,33 @@ +diff --git a/Makefile b/Makefile +index edd2c4a..73b25ea 100644 +--- a/Makefile ++++ b/Makefile +@@ -30,8 +30,8 @@ all: $(PROG) $(TEST_PROG) + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.4.1 +-include $(HTSDIR)/htslib.mk +-include $(HTSDIR)/htslib_static.mk ++#include $(HTSDIR)/htslib.mk ++#include $(HTSDIR)/htslib_static.mk + HTSLIB = $(HTSDIR)/libhts.a + BGZIP = $(HTSDIR)/bgzip + TABIX = $(HTSDIR)/tabix +@@ -73,7 +73,7 @@ GSL_LIBS = + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -217,7 +217,7 @@ test/test-regidx.o: test/test-regidx.c regidx.h + test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) + + doc/bcftools.1: doc/bcftools.txt -- cgit v1.2.3 From bca2c57658db1fdccca996cd59a3b43f739f0d87 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 26 Jun 2017 21:07:10 +1000 Subject: gnu: bamm: Use htslib-1.3. * gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3. --- gnu/packages/bioinformatics.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87da4aed15..53239cb697 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -248,7 +248,7 @@ structure of the predicted RNA.") ("python-nose" ,python2-nose) ("python-pysam" ,python2-pysam))) (inputs - `(("htslib" ,htslib) + `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. ("samtools" ,samtools) ("bwa" ,bwa) ("grep" ,grep) @@ -3079,6 +3079,20 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +;; This package should be removed once no packages rely upon it. +(define htslib-1.3 + (package + (inherit htslib) + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) + (define-public idr (package (name "idr") -- cgit v1.2.3 From 60739965daf61150f07c7a505d682e65190733e0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 7 Apr 2017 22:07:45 +1000 Subject: gnu: python-pysam: Update to 0.11.2.2. * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2. --- 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 53239cb697..ee317e5bc9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1418,7 +1418,7 @@ multiple sequence alignments.") (define-public python-pysam (package (name "python-pysam") - (version "0.10.0") + (version "0.11.2.2") (source (origin (method url-fetch) ;; Test data is missing on PyPi. @@ -1428,7 +1428,7 @@ multiple sequence alignments.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1mmvn91agr238kwz7226xq0i7k84lg2nxywn9712mzj7gvgqhfy8")) + "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc")) (modules '((guix build utils))) (snippet ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. -- cgit v1.2.3 From 4fb6d1280ec273c58812f0448c63717a90463745 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 27 Jun 2017 08:18:04 +1000 Subject: gnu: htslib: Update to 1.5. * gnu/packages/bioinformatics.scm (htslib): Update to 1.5. --- 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 ee317e5bc9..0447626a4a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3045,7 +3045,7 @@ manipulating HTS data.") (define-public htslib (package (name "htslib") - (version "1.4.1") + (version "1.5") (source (origin (method url-fetch) (uri (string-append @@ -3053,7 +3053,7 @@ manipulating HTS data.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1crkk79kgxcmrkmh5f58c4k93w4rz6lp97sfsq3s6556zxcxvll5")))) + "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 63fa0ffcd43484c2d7dcf32866529c022309ff20 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 27 Jun 2017 08:22:25 +1000 Subject: gnu: samtools: Update to 1.5. * gnu/packages/bioinformatics.scm (samtools): Update to 1.5. --- 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 0447626a4a..3e3aaeb657 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4524,7 +4524,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.4.1") + (version "1.5") (source (origin (method url-fetch) @@ -4533,7 +4533,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "0vzxjm5vkgvzynl7cssm1l560rqs2amdaib1x8sp2ch9b7bxx9xx")))) + "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) -- cgit v1.2.3 From 0620387a594be1e8069dea8cda83dfc4a0b7f2de Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 22 Jul 2017 20:36:44 +1000 Subject: gnu: bcftools: Update to 1.5. * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 10 +++---- gnu/packages/patches/bcftools-fix-makefile.patch | 33 ------------------------ 3 files changed, 5 insertions(+), 39 deletions(-) delete mode 100644 gnu/packages/patches/bcftools-fix-makefile.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 3397216e15..8d3916e26d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -522,7 +522,6 @@ dist_patch_DATA = \ %D%/packages/patches/awesome-reproducible-png.patch \ %D%/packages/patches/azr3.patch \ %D%/packages/patches/bash-completion-directories.patch \ - %D%/packages/patches/bcftools-fix-makefile.patch \ %D%/packages/patches/binutils-ld-new-dtags.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/binutils-mips-bash-bug.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e3aaeb657..d9f7e2a5e1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -300,7 +300,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.4.1") + (version "1.5") (source (origin (method url-fetch) (uri (string-append @@ -308,18 +308,19 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "024xv59bzv148b6w3das4jmldf7rywsf8y1fbqznap008qc8gl6p")) - (patches (search-patches "bcftools-fix-makefile.patch")) + "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) (modules '((guix build utils))) (snippet ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.4.1")))) + '(delete-file-recursively "htslib-1.5")))) (build-system gnu-build-system) (arguments `(#:test-target "test" + #:configure-flags (list "--with-htslib=system") #:make-flags (list "USE_GPL=1" + "LIBS=-lgsl -lgslcblas" (string-append "prefix=" (assoc-ref %outputs "out")) (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") @@ -328,7 +329,6 @@ BAM files.") (string-append "PACKAGE_VERSION=" ,version)) #:phases (modify-phases %standard-phases - (delete 'configure) (add-before 'check 'patch-tests (lambda _ (substitute* "test/test.pl" diff --git a/gnu/packages/patches/bcftools-fix-makefile.patch b/gnu/packages/patches/bcftools-fix-makefile.patch deleted file mode 100644 index 614f5fd6bd..0000000000 --- a/gnu/packages/patches/bcftools-fix-makefile.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff --git a/Makefile b/Makefile -index edd2c4a..73b25ea 100644 ---- a/Makefile -+++ b/Makefile -@@ -30,8 +30,8 @@ all: $(PROG) $(TEST_PROG) - - # Adjust $(HTSDIR) to point to your top-level htslib directory - HTSDIR = htslib-1.4.1 --include $(HTSDIR)/htslib.mk --include $(HTSDIR)/htslib_static.mk -+#include $(HTSDIR)/htslib.mk -+#include $(HTSDIR)/htslib_static.mk - HTSLIB = $(HTSDIR)/libhts.a - BGZIP = $(HTSDIR)/bgzip - TABIX = $(HTSDIR)/tabix -@@ -73,7 +73,7 @@ GSL_LIBS = - ifdef USE_GPL - EXTRA_CPPFLAGS += -DUSE_GPL - OBJS += polysomy.o peakfit.o -- GSL_LIBS = -lgsl -lcblas -+ GSL_LIBS = -lgsl -lgslcblas - endif - - prefix = /usr/local -@@ -217,7 +217,7 @@ test/test-regidx.o: test/test-regidx.c regidx.h - test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) - --bcftools: $(HTSLIB) $(OBJS) -+bcftools: $(OBJS) - $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) - - doc/bcftools.1: doc/bcftools.txt -- cgit v1.2.3 From 897ab082b23109d7710ff11bb18360153295bed2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 27 Jun 2017 11:16:40 +1000 Subject: gnu: python-plastid: Update to 0.4.8. * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8. --- 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 d9f7e2a5e1..eab9d49e12 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1527,13 +1527,13 @@ UCSC genome browser.") (define-public python-plastid (package (name "python-plastid") - (version "0.4.6") + (version "0.4.8") (source (origin (method url-fetch) (uri (pypi-uri "plastid" version)) (sha256 (base32 - "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj")))) + "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8")))) (build-system python-build-system) (arguments ;; Some test files are not included. -- cgit v1.2.3 From f3f68a442c1c40438078c24c0869e22c08f30c48 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 15 Jul 2017 16:31:40 +1000 Subject: gnu: metabat: Update to 2.11.1. * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 89 +++++++++++----------- gnu/packages/patches/metabat-fix-compilation.patch | 39 ++++++++++ 3 files changed, 83 insertions(+), 46 deletions(-) create mode 100644 gnu/packages/patches/metabat-fix-compilation.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 8d3916e26d..3eccc879b0 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -840,6 +840,7 @@ dist_patch_DATA = \ %D%/packages/patches/mesa-skip-disk-cache-test.patch \ %D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch \ %D%/packages/patches/metabat-remove-compilation-date.patch \ + %D%/packages/patches/metabat-fix-compilation.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \ %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch \ %D%/packages/patches/mpc123-initialize-ao.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eab9d49e12..3b4cc359ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3467,23 +3467,20 @@ form of assemblies or reads.") license:cpl1.0)))) ; Open Bloom Filter (define-public metabat - ;; We package from a git commit because compilation of the released version - ;; fails. - (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b")) - (package - (name "metabat") - (version (string-append "0.32.4-1." (string-take commit 8))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://bitbucket.org/berkeleylab/metabat.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr")) - (patches (search-patches "metabat-remove-compilation-date.patch")))) + (package + (name "metabat") + (version "2.11.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9")) + (patches (search-patches "metabat-remove-compilation-date.patch" + "metabat-fix-compilation.patch")))) (build-system gnu-build-system) (arguments `(#:phases @@ -3500,35 +3497,35 @@ form of assemblies or reads.") "#include \"htslib/kseq.h\"")) #t)) (add-after 'unpack 'fix-scons - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "SConstruct" - (("^htslib_dir = 'samtools'") - (string-append "hitslib_dir = '" - (assoc-ref inputs "htslib") - "'")) - (("^samtools_dir = 'samtools'") - (string-append "samtools_dir = '" - (assoc-ref inputs "htslib") - "'")) - (("^findStaticOrShared\\('bam', hts_lib") - (string-append "findStaticOrShared('bam', '" - (assoc-ref inputs "samtools") - "/lib'")) - ;; Do not distribute README. - (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) - #t)) + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "SConstruct" + (("^htslib_dir += 'samtools'") + (string-append "htslib_dir = '" + (assoc-ref inputs "htslib") + "'")) + (("^samtools_dir = 'samtools'") + (string-append "samtools_dir = '" + (assoc-ref inputs "samtools") + "'")) + (("^findStaticOrShared\\('bam', hts_lib") + (string-append "findStaticOrShared('bam', '" + (assoc-ref inputs "samtools") + "/lib'")) + ;; Do not distribute README. + (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) + #t)) (delete 'configure) (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (mkdir (assoc-ref outputs "out")) - (zero? (system* "scons" - (string-append - "PREFIX=" - (assoc-ref outputs "out")) - (string-append - "BOOST_ROOT=" - (assoc-ref inputs "boost")) - "install")))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (mkdir (assoc-ref outputs "out")) + (zero? (system* "scons" + (string-append + "PREFIX=" + (assoc-ref outputs "out")) + (string-append + "BOOST_ROOT=" + (assoc-ref inputs "boost")) + "install")))) ;; Check and install are carried out during build phase. (delete 'check) (delete 'install)))) @@ -3549,8 +3546,8 @@ sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. MetaBAT is an automated metagenome binning software, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.") - (license (license:non-copyleft "file://license.txt" - "See license.txt in the distribution."))))) + (license (license:non-copyleft "file://license.txt" + "See license.txt in the distribution.")))) (define-public minced (package diff --git a/gnu/packages/patches/metabat-fix-compilation.patch b/gnu/packages/patches/metabat-fix-compilation.patch new file mode 100644 index 0000000000..7086a96e86 --- /dev/null +++ b/gnu/packages/patches/metabat-fix-compilation.patch @@ -0,0 +1,39 @@ +This patch changes metabat so that (1) it is not build statically, (2) it uses +shared libraries rather than static libraries where possible. + +diff --git a/SConstruct b/SConstruct +index 69cdc0a..ac99bcb 100644 +--- a/SConstruct ++++ b/SConstruct +@@ -26,8 +26,6 @@ debug = ARGUMENTS.get('DEBUG', None) + build_flags = ['-Wall', '-g', '-std=c++11', '-fopenmp'] + link_flags = ['-lstdc++', '-lm', '-fopenmp'] + +-if platform.platform(True, True).find('Darwin') == -1: +- link_flags.extend(['-static', '-static-libgcc', '-static-libstdc++']) + + if debug is None: + build_flags.extend(['-O3', '-DNDEBUG', '-Wno-unknown-pragmas', '-Wno-deprecated-declarations', '-Wno-overflow', '-Wno-unused-variable']) +@@ -110,17 +108,17 @@ def findStaticOrShared( lib, testPaths, static_source_list, link_flag_list, stat + for path in testPaths: + if not os.path.isdir(path): + continue ++ for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)): ++ if os.path.isfile(testfile): ++ print "Found shared library %s as %s" % (lib, testfile) ++ link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] ) ++ return + for suffix in staticSuffixes: + testfile = '%s/lib%s%s' % (path, lib, suffix) + if os.path.isfile(testfile): + static_source_list.append(testfile) + print "Found static library %s as %s" % (lib, testfile) + return +- for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)): +- if os.path.isfile(testfile): +- print "Found shared library %s as %s" % (lib, testfile) +- link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] ) +- return + print "Could not find library for %s!!! Looked in %s" % (lib, testPaths) + return + -- cgit v1.2.3