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-rw-r--r--gnu/packages/bioinformatics.scm143
1 files changed, 105 insertions, 38 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0fe0624aff..0e9e6b13fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2030,10 +2030,57 @@ 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")
- (version "0.9.18")
+ (version "0.9.19")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2042,7 +2089,7 @@ 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
@@ -3623,7 +3670,7 @@ data.")
(define-public kaiju
(package
(name "kaiju")
- (version "1.5.0")
+ (version "1.6.2")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3632,7 +3679,7 @@ data.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
+ "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
@@ -3650,7 +3697,8 @@ data.")
(copy-recursively "util" bin))
#t)))))
(inputs
- `(("perl" ,perl)))
+ `(("perl" ,perl)
+ ("zlib" ,zlib)))
(home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification
@@ -3688,7 +3736,7 @@ 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
@@ -3697,7 +3745,7 @@ 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
@@ -3774,7 +3822,7 @@ sequences).")
(define-public mash
(package
(name "mash")
- (version "1.1.1")
+ (version "2.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3783,7 +3831,7 @@ sequences).")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
+ "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
(modules '((guix build utils)))
(snippet
;; Delete bundled kseq.
@@ -3801,7 +3849,9 @@ 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))
@@ -6062,14 +6112,14 @@ data types as well.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.56.1")
+ (version "1.56.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq"))))
+ "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -6871,8 +6921,7 @@ also known as views, in a controlled vocabulary.")
("r-rmarkdown" ,r-rmarkdown)
("r-tinytex" ,r-tinytex)
("r-yaml" ,r-yaml)
- ("r-xfun" ,r-xfun)
- ("ghc-pandoc" ,ghc-pandoc)))
+ ("r-xfun" ,r-xfun)))
(home-page "https://github.com/rstudio/bookdown")
(synopsis "Authoring books and technical documents with R markdown")
(description "This package provides output formats and utilities for
@@ -8511,14 +8560,14 @@ library implementing most of the pipeline's features.")
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.4.2")
+ (version "1.4.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"))))
+ "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -8528,7 +8577,6 @@ library implementing most of the pipeline's features.")
("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
("r-iranges" ,r-iranges)
("r-nmf" ,r-nmf)
("r-plyr" ,r-plyr)
@@ -10939,12 +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)
@@ -10953,34 +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
@@ -10993,8 +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
@@ -11005,7 +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)))