diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 103 |
1 files changed, 42 insertions, 61 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f89c60b8cd..245e7dd564 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3760,13 +3760,13 @@ experiments.") (define-public macs (package (name "macs") - (version "2.1.0.20151222") + (version "2.1.1.20160309") (source (origin (method url-fetch) (uri (pypi-uri "MACS2" version)) (sha256 (base32 - "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) + "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210")))) (build-system python-build-system) (arguments `(#:python ,python-2 ; only compatible with Python 2.7 @@ -7058,28 +7058,6 @@ functionality.") checks on R packages that are to be submitted to the Bioconductor repository.") (license license:artistic2.0))) -(define-public r-getopt - (package - (name "r-getopt") - (version "1.20.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "getopt" version)) - (sha256 - (base32 - "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x")))) - (build-system r-build-system) - (home-page "https://github.com/trevorld/getopt") - (synopsis "Command-line option processor for R") - (description - "This package is designed to be used with Rscript to write shebang -scripts that accept short and long options. Many users will prefer to -use the packages @code{optparse} or @code{argparse} which add extra -features like automatically generated help options and usage texts, -support for default values, positional argument support, etc.") - (license license:gpl2+))) - (define-public r-optparse (package (name "r-optparse") @@ -12831,7 +12809,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.3") + (version "0.0.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -12839,7 +12817,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "0pz080k4ajlc4rlznkn3najy2a6874gb56rf9g4ag9wqz31q174j")))) + "16gla23rmziimqan7w494q0nr7vfbp42zzkrl9fracmr4k7b1kzr")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -12851,14 +12829,6 @@ once. This package provides tools to perform Drop-seq analyses.") (substitute* "Makefile.in" (("(^ tests/test_trim_galore/test.sh).*" _ m) m) (("^ test.sh") "")) - #t)) - (add-after 'install 'wrap-executable - ;; Make sure the executable finds all R modules. - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/pigx-rnaseq") - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) - `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) #t))))) (inputs `(("gzip" ,gzip) @@ -12906,7 +12876,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.17") + (version "0.0.20") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12914,7 +12884,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "1c0x5lswvc8v9fw4iynl5rcfs7h7clzp4hqdnl65ia7rk35n4zg9")))) + "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3")))) (build-system gnu-build-system) ;; parts of the tests rely on access to the network (arguments '(#:tests? #f)) @@ -12976,7 +12946,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.9") + (version "0.0.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -12984,7 +12954,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "0j1dfjk8m1p1h6d5yw63scjlbx56z8gixmbw626w1vcyblg0frmz")))) + "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy")))) (build-system gnu-build-system) (arguments `(#:phases @@ -12996,14 +12966,6 @@ in an easily configurable manner.") (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")) - #t)) - (add-after 'install 'wrap-executable - ;; Make sure the executable finds all R modules. - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/pigx-bsseq") - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) - `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) #t))))) (native-inputs `(("tzdata" ,tzdata))) @@ -13043,7 +13005,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.5") + (version "0.0.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -13051,24 +13013,14 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "0a73rilv0vnw42d5rsdq205h4f0x8j3jqv998janh4s324c6w2kj")))) + "0fvdymnka598z2ka7zk6rwrf9dq89p5lyd2y9swvyg72hn1jwjai")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") "/share/java/picard.jar") (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") - "/share/java/dropseq.jar")) - #:phases - (modify-phases %standard-phases - (add-after 'install 'wrap-executable - ;; Make sure the executable finds all R modules. - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/pigx-scrnaseq") - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) - `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) - #t))))) + "/share/java/dropseq.jar")))) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) @@ -13123,7 +13075,7 @@ based methods.") (define-public pigx (package (name "pigx") - (version "0.0.2") + (version "0.0.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" @@ -13131,7 +13083,7 @@ based methods.") "/pigx-" version ".tar.gz")) (sha256 (base32 - "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8")))) + "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7")))) (build-system gnu-build-system) (inputs `(("python" ,python) @@ -13296,3 +13248,32 @@ cases include: divergence below ~15%. @end enumerate\n") (license license:expat))) + +(define-public r-loomr + (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") + (revision "1")) + (package + (name "r-loomr") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mojaveazure/loomR.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-r6" ,r-r6) + ("r-hdf5r" ,r-hdf5r) + ("r-iterators" ,r-iterators) + ("r-itertools" ,r-itertools) + ("r-matrix" ,r-matrix))) + (home-page "https://github.com/mojaveazure/loomR") + (synopsis "R interface for loom files") + (description "This package provides an R interface to access, create, +and modify loom files. loomR aims to be completely compatible with loompy.") + (license license:gpl3)))) |