diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 124 |
1 files changed, 49 insertions, 75 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f60a918d75..957c88d0c6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> +;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,6 +54,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) + #:use-module (guix deprecation) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) @@ -941,7 +943,9 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) + ;; FIXME: Upgrade to pandas 1.0 when + ;; https://github.com/biocore/biom-format/issues/837 is resolved. + ("python-pandas" ,python-pandas-0.25))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) @@ -2406,12 +2410,18 @@ interval trees with associated meta-data. It is primarily used by the (name "python-deeptools") (version "3.4.3") (source (origin - (method url-fetch) - (uri (pypi-uri "deepTools" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/deepTools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -2421,7 +2431,7 @@ interval trees with associated meta-data. It is primarily used by the ("python-pysam" ,python-pysam) ("python-scipy" ,python-scipy) ("python-deeptoolsintervals" ,python-deeptoolsintervals) - ("python-plotly" ,python-plotly))) + ("python-plotly" ,python-plotly-2.4.1))) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts @@ -2436,6 +2446,8 @@ annotations of the genome.") ;; remainder of the code is licensed under the MIT license. (license (list license:bsd-3 license:expat)))) +(define-deprecated deeptools python-deeptools) + (define-public cutadapt (package (name "cutadapt") @@ -2599,51 +2611,6 @@ trees (phylogenies) and characters.") with Python.") (license license:expat))) -(define-public deeptools - (package - (name "deeptools") - (version "3.1.3") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/deepTools.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This phase fails, but it's not needed. - (delete 'reset-gzip-timestamps)))) - (inputs - `(("python-plotly" ,python-plotly) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig))) - (native-inputs - `(("python-mock" ,python-mock) ;for tests - ("python-nose" ,python-nose) ;for tests - ("python-pytz" ,python-pytz))) ;for tests - (home-page "https://github.com/deeptools/deepTools") - (synopsis "Tools for normalizing and visualizing deep-sequencing data") - (description - "DeepTools addresses the challenge of handling the large amounts of data -that are now routinely generated from DNA sequencing centers. To do so, -deepTools contains useful modules to process the mapped reads data to create -coverage files in standard bedGraph and bigWig file formats. By doing so, -deepTools allows the creation of normalized coverage files or the comparison -between two files (for example, treatment and control). Finally, using such -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") @@ -3050,16 +3017,16 @@ dynamic programming or a variety of heuristics.") (define-public express (package (name "express") - (version "1.5.1") + (version "1.5.3") (source (origin - (method url-fetch) - (uri - (string-append - "http://bio.math.berkeley.edu/eXpress/downloads/express-" - version "/express-" version "-src.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/adarob/eXpress.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) + "18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -3076,6 +3043,12 @@ dynamic programming or a variety of heuristics.") (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") (string-append (assoc-ref inputs "bamtools") "/lib")) (("libprotobuf.a") "libprotobuf.so")) + #t)) + (add-after 'unpack 'remove-update-check + (lambda _ + (substitute* "src/main.cpp" + (("#include \"update_check.h\"") "") + (("check_version\\(PACKAGE_VERSION\\);") "")) #t))))) (inputs `(("boost" ,boost) @@ -7716,13 +7689,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.24.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0ab92nq7lvhvhgp512qhiiphpby0b17c666qska6p8a636zzmqiv")))) + "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7813,13 +7786,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.44.1") + (version "3.44.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0l6f6lz1rghj8c5s14ljbnmsrwz27fi6a7g42n15n3d3msvflw36")))) + "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7950,13 +7923,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.44.0") + (version "2.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0ag26q9283p9mfz4zx8qnx1w7b7ilmsb8wyx737z9cqy9a0i57wj")))) + "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8923,13 +8896,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "097znwl95y2vd6asyqxs62m7binwxqmna7ss0302yl3b0s72skcy")))) + "102zam2j43jwgaz9ch6y2jjbc3qf56ngmggikf99s8l3w9ggbskm")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -10840,14 +10813,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1g848s0qc6i4ipd7y2s5pk8k1xggk2kfy0gnr8wjjs2gq3914aw4")))) + "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -13437,14 +13410,14 @@ cases include: (name "miniasm") (version "0.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/lh3/miniasm/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lh3/miniasm") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 - "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v")))) + (base32 + "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -13457,7 +13430,8 @@ cases include: (lambda* (#:key inputs outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "miniasm" bin) - (install-file "minidot" bin))))))) + (install-file "minidot" bin) + #t)))))) (home-page "https://github.com/lh3/miniasm") (synopsis "Ultrafast de novo assembly for long noisy reads") (description "Miniasm is a very fast OLC-based de novo assembler for noisy |