diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 379 |
1 files changed, 314 insertions, 65 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 314aaa4077..f0b589b6c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -39,6 +40,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system r) #:use-module (guix build-system ruby) + #:use-module (guix build-system scons) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages autotools) @@ -2961,7 +2963,7 @@ from high-throughput sequencing assays.") (define-public java-htsjdk (package (name "java-htsjdk") - (version "1.129") + (version "2.3.0") ; last version without build dependency on gradle (source (origin (method url-fetch) (uri (string-append @@ -2970,15 +2972,18 @@ from high-throughput sequencing assays.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) + "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) (modules '((guix build utils))) - ;; remove build dependency on git - (snippet '(substitute* "build.xml" - (("failifexecutionfails=\"true\"") - "failifexecutionfails=\"false\""))))) + (snippet + ;; Delete pre-built binaries + '(begin + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) (build-system ant-build-system) (arguments `(#:tests? #f ; test require Internet access + #:jdk ,icedtea-8 #:make-flags (list (string-append "-Ddist=" (assoc-ref %outputs "out") "/share/java/htsjdk/")) @@ -2987,6 +2992,15 @@ from high-throughput sequencing assays.") (modify-phases %standard-phases ;; The build phase also installs the jars (delete 'install)))) + (inputs + `(("java-ngs" ,java-ngs) + ("java-snappy-1" ,java-snappy-1) + ("java-commons-compress" ,java-commons-compress) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-xz" ,java-xz))) + (native-inputs + `(("java-testng" ,java-testng))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -2996,6 +3010,198 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +;; This version matches java-htsjdk 2.3.0. Later versions also require a more +;; recent version of java-htsjdk, which depends on gradle. +(define-public java-picard + (package + (name "java-picard") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-built binaries. + (delete-file-recursively "lib") + (mkdir-p "lib") + (substitute* "build.xml" + ;; Remove build-time dependency on git. + (("failifexecutionfails=\"true\"") + "failifexecutionfails=\"false\"") + ;; Use our htsjdk. + (("depends=\"compile-htsjdk, ") + "depends=\"") + (("depends=\"compile-htsjdk-tests, ") + "depends=\"") + ;; Build picard-lib.jar before building picard.jar + (("name=\"picard-jar\" depends=\"" line) + (string-append line "picard-lib-jar, "))) + #t)))) + (build-system ant-build-system) + (arguments + `(#:build-target "picard-jar" + #:test-target "test" + ;; Tests require jacoco:coverage. + #:tests? #f + #:make-flags + (list (string-append "-Dhtsjdk_lib_dir=" + (assoc-ref %build-inputs "java-htsjdk") + "/share/java/htsjdk/") + "-Dhtsjdk-classes=dist/tmp" + (string-append "-Dhtsjdk-version=" + ,(package-version java-htsjdk))) + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-our-htsjdk + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("\\$\\{htsjdk\\}/lib") + (string-append (assoc-ref inputs "java-htsjdk") + "/share/java/htsjdk/"))) + #t)) + (add-after 'unpack 'make-test-target-independent + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("name=\"test\" depends=\"compile, ") + "name=\"test\" depends=\"")) + #t)) + (replace 'install (install-jars "dist"))))) + (inputs + `(("java-htsjdk" ,java-htsjdk) + ("java-guava" ,java-guava))) + (native-inputs + `(("java-testng" ,java-testng))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "Tools for manipulating high-throughput sequencing data and formats") + (description "Picard is a set of Java command line tools for manipulating +high-throughput sequencing (HTS) data and formats. Picard is implemented +using the HTSJDK Java library to support accessing file formats that are +commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and +VCF.") + (license license:expat))) + +;; This is the last version of Picard to provide net.sf.samtools +(define-public java-picard-1.113 + (package (inherit java-picard) + (name "java-picard") + (version "1.113") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-built binaries. + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) + (build-system ant-build-system) + (arguments + `(#:build-target "picard-jar" + #:test-target "test" + ;; FIXME: the class path at test time is wrong. + ;; [testng] Error: A JNI error has occurred, please check your installation and try again + ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException + #:tests? #f + #:jdk ,icedtea-8 + ;; This is only used for tests. + #:make-flags + (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") + #:phases + (modify-phases %standard-phases + ;; Do not use bundled ant bzip2. + (add-after 'unpack 'use-ant-bzip + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") + (string-append (assoc-ref inputs "ant") + "/lib/ant.jar"))) + #t)) + (add-after 'unpack 'make-test-target-independent + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("name=\"test\" depends=\"compile, ") + "name=\"test\" depends=\"compile-tests, ") + (("name=\"compile\" depends=\"compile-src, compile-tests\"") + "name=\"compile\" depends=\"compile-src\"")) + #t)) + (add-after 'unpack 'fix-deflater-path + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "src/java/net/sf/samtools/Defaults.java" + (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") + (string-append "getStringProperty(\"intel_deflater_so_path\", \"" + (assoc-ref outputs "out") + "/lib/jni/libIntelDeflater.so" + "\")"))) + #t)) + ;; Build the deflater library, because we've previously deleted the + ;; pre-built one. This can only be built with access to the JDK + ;; sources. + (add-after 'build 'build-jni + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "lib/jni") + (mkdir-p "jdk-src") + (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" + "-xf" (assoc-ref inputs "jdk-src"))) + (zero? (system* "javah" "-jni" + "-classpath" "classes" + "-d" "lib/" + "net.sf.samtools.util.zip.IntelDeflater")) + (with-directory-excursion "src/c/inteldeflater" + (zero? (system* "gcc" "-I../../../lib" "-I." + (string-append "-I" (assoc-ref inputs "jdk") + "/include/linux") + "-I../../../jdk-src/src/share/native/common/" + "-I../../../jdk-src/src/solaris/native/common/" + "-c" "-O3" "-fPIC" "IntelDeflater.c")) + (zero? (system* "gcc" "-shared" + "-o" "../../../lib/jni/libIntelDeflater.so" + "IntelDeflater.o" "-lz" "-lstdc++")))))) + ;; We can only build everything else after building the JNI library. + (add-after 'build-jni 'build-rest + (lambda* (#:key make-flags #:allow-other-keys) + (zero? (apply system* `("ant" "all" ,@make-flags))))) + (add-before 'build 'set-JAVA6_HOME + (lambda _ + (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) + #t)) + (replace 'install (install-jars "dist")) + (add-after 'install 'install-jni-lib + (lambda* (#:key outputs #:allow-other-keys) + (let ((jni (string-append (assoc-ref outputs "out") + "/lib/jni"))) + (mkdir-p jni) + (install-file "lib/jni/libIntelDeflater.so" jni) + #t)))))) + (inputs + `(("java-snappy-1" ,java-snappy-1) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-cofoja" ,java-cofoja) + ("ant" ,ant) ; for bzip2 support at runtime + ("zlib" ,zlib))) + (native-inputs + `(("ant-apache-bcel" ,ant-apache-bcel) + ("ant-junit" ,ant-junit) + ("java-testng" ,java-testng) + ("java-commons-bcel" ,java-commons-bcel) + ("java-jcommander" ,java-jcommander) + ("jdk" ,icedtea-8 "jdk") + ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) + (define-public htslib (package (name "htslib") @@ -3050,7 +3256,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") (define-public idr (package (name "idr") - (version "2.0.0") + (version "2.0.3") (source (origin (method url-fetch) (uri (string-append @@ -3059,10 +3265,15 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) + "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3")) + ;; Delete generated C code. + (snippet + '(begin (delete-file "idr/inv_cdf.c") #t)))) (build-system python-build-system) - (arguments - `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" + ;; There is only one test ("test_inv_cdf.py") and it tests features that + ;; are no longer part of this package. It also asserts False, which + ;; causes the tests to always fail. + (arguments `(#:tests? #f)) (propagated-inputs `(("python-scipy" ,python-scipy) ("python-sympy" ,python-sympy) @@ -3076,12 +3287,12 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.") - (license license:gpl3+))) + (license license:gpl2+))) (define-public jellyfish (package (name "jellyfish") - (version "2.2.4") + (version "2.2.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/gmarcais/Jellyfish/" @@ -3089,7 +3300,7 @@ experiments and provide highly stable thresholds based on reproducibility.") "/jellyfish-" version ".tar.gz")) (sha256 (base32 - "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk")))) + "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q")))) (build-system gnu-build-system) (outputs '("out" ;for library "ruby" ;for Ruby bindings @@ -3112,7 +3323,10 @@ experiments and provide highly stable thresholds based on reproducibility.") `(("bc" ,bc) ("time" ,time) ("ruby" ,ruby) - ("python" ,python-2))) + ("python" ,python-2) + ("pkg-config" ,pkg-config))) + (inputs + `(("htslib" ,htslib))) (synopsis "Tool for fast counting of k-mers in DNA") (description "Jellyfish is a tool for fast, memory-efficient counting of k-mers in @@ -3434,9 +3648,14 @@ form of assemblies or reads.") (base32 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) (patches (search-patches "metabat-fix-compilation.patch")))) - (build-system gnu-build-system) + (build-system scons-build-system) (arguments - `(#:phases + `(#:scons ,scons-python2 + #:scons-flags + (list (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost"))) + #:tests? #f ;; Tests are run during the build phase. + #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-includes (lambda _ @@ -3466,30 +3685,13 @@ form of assemblies or reads.") "/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")))) - ;; Check and install are carried out during build phase. - (delete 'check) - (delete 'install)))) + #t))))) (inputs `(("zlib" ,zlib) ("perl" ,perl) ("samtools" ,samtools) ("htslib" ,htslib) ("boost" ,boost))) - (native-inputs - `(("scons" ,scons))) (home-page "https://bitbucket.org/berkeleylab/metabat") (synopsis "Reconstruction of single genomes from complex microbial communities") @@ -5412,14 +5614,14 @@ sequences.") (define-public subread (package (name "subread") - (version "1.5.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/subread/subread-" version "/subread-" version "-source.tar.gz")) (sha256 (base32 - "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy")))) + "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target @@ -5676,14 +5878,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0wlrp3v2jxw9is98ap39dfi7z97kmw1wv1xi4h7yfh12zpj2r8l0")))) + "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5700,6 +5902,29 @@ data types as well.") microarrays.") (license license:artistic2.0))) +(define-public r-copynumber + (package + (name "r-copynumber") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "copynumber" version)) + (sha256 + (base32 + "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomicranges" ,r-genomicranges) + ("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/copynumber") + (synopsis "Segmentation of single- and multi-track copy number data") + (description + "This package segments single- and multi-track copy number data by a +penalized least squares regression method.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") @@ -5755,14 +5980,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1hcxnkkjfvz4hj8iqidshwsjq7jnl1z7wj63dvcwlx1zx5aichyh")))) + "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5792,14 +6017,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0qxwnz2ffhav9slcn095k206cfza9i3i5l7w1154plf08gpy1d1d")))) + "1hwckj4ijgpdchbakvh60nmcaz4fwd5yplhn0880z3dnlsrp8ik3")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -5886,14 +6111,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0kpkl6c5lrar6ip7wlhvd5axqlb9lb5l3lgbdb3dlih32c3nz0yq")))) + "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -6541,14 +6766,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-getopt (package (name "r-getopt") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 - "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r")))) + "0m463mcvixh54i3ng42n0vxmdlf97dgbfs2sf9wnjm782ddw68hm")))) (build-system r-build-system) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") @@ -6768,13 +6993,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.24.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1lllp2vgyfbrar1yg28ji7am470hfzrzxm1bgdk68xpnrwcgcl25")))) + "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6806,13 +7031,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.0") + (version "3.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0a15gsaky0hfrkx8wrrmp0labzxpq6m2hrd33zl206wyas8bqzcs")))) + "1zyw01z9crm1jc86fva4pqxd9zxfsbsqwjq6ry39gag9pfb7pwcz")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7127,13 +7352,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0sw30lj11wv7ifzypqm04lcah987crqwvj48wz3flaw3biw41zfi")))) + "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -8098,14 +8323,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0sqbrswg8ylkjb9q3vqcb5ggwixynwj6hyv2n4sk7snyk61z3fq9")))) + "1qhxlfl85ifr30wrsidcn3kca3vs8fd8cmwd82gvgx9ppww8vs06")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8311,11 +8536,6 @@ of gene-level counts.") (lambda* (#:key outputs #:allow-other-keys) (system* "tar" "-xzvf" "src/hdf5source/hdf5small.tgz" "-C" "src/" ) - (substitute* "src/Makevars" - (("^.*cd hdf5source &&.*$") "") - (("^.*gunzip -dc hdf5small.tgz.*$") "") - (("^.*rm -rf hdf5.*$") "") - (("^.*mv hdf5source/hdf5 ..*$") "")) (substitute* "src/hdf5/configure" (("/bin/mv") "mv")) #t))))) @@ -8851,14 +9071,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.16.4") + (version "1.17") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "1pmhsfvd45a44xdiml4zx3zd5fhygqyziqvygahkk9yibnyhv4cv")))) + "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/MALDIquant") @@ -9132,14 +9352,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.11.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1vi4ngwbayrv2jkfb4pbmdp37xn04y07rh1jcklqfh0fcrm1jdig")))) + "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9370,14 +9590,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1arfka3czw8hkv6n2d85bgibq81s2rgkwhmpaxzhy6nw39vv7y8b")))) + "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10859,3 +11079,32 @@ contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data.") ;; GPLv3 only (license license:gpl3))) + +(define-public kallisto + (package + (name "kallisto") + (version "0.43.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pachterlab/" + "kallisto/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; no "check" target + (inputs + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) + (home-page "http://pachterlab.github.io/kallisto/") + (synopsis "Near-optimal RNA-Seq quantification") + (description + "Kallisto is a program for quantifying abundances of transcripts from +RNA-Seq data, or more generally of target sequences using high-throughput +sequencing reads. It is based on the novel idea of pseudoalignment for +rapidly determining the compatibility of reads with targets, without the need +for alignment. Pseudoalignment of reads preserves the key information needed +for quantification, and kallisto is therefore not only fast, but also as +accurate as existing quantification tools.") + (license license:bsd-2))) |