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-rw-r--r--gnu/packages/bioinformatics.scm379
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)))
generated by cgit v1.2.3 (git 2.25.4) at 2024-06-29 03:47:02 +0000