diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 143 |
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))) |