diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 114 |
1 files changed, 92 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d4380f86ac..5af4947b68 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2039,10 +2039,57 @@ 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 @@ -2051,7 +2098,7 @@ 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 @@ -3698,7 +3745,7 @@ 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 @@ -3707,7 +3754,7 @@ 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 @@ -3784,7 +3831,7 @@ sequences).") (define-public mash (package (name "mash") - (version "1.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (string-append @@ -3793,7 +3840,7 @@ sequences).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) + "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) (modules '((guix build utils))) (snippet '(begin @@ -3813,7 +3860,9 @@ 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)) @@ -10960,34 +11009,41 @@ 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 @@ -11000,8 +11056,9 @@ 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 @@ -11012,7 +11069,20 @@ 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))) |