diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 294 |
1 files changed, 164 insertions, 130 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f8551b7723..48623d2cce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -830,14 +830,18 @@ provides the Ribotaper pipeline.") `(#:python ,python-2 #:phases (modify-phases %standard-phases + ;; This test fails because of the matplotlib plotting backend. + (add-after 'unpack 'disable-plot-test + (lambda _ + (substitute* "src/ribodiff/functional_test_te.py" + (("pl\\.make_plots\\(data, opts\\)") "#")))) ;; Generate an installable executable script wrapper. (add-after 'unpack 'patch-setup.py (lambda _ (substitute* "setup.py" (("^(.*)packages=.*" line prefix) (string-append line "\n" - prefix "scripts=['scripts/TE.py'],\n"))) - #t))))) + prefix "scripts=['scripts/TE.py'],\n")))))))) (inputs `(("python-numpy" ,python2-numpy) ("python-matplotlib" ,python2-matplotlib) @@ -1013,7 +1017,7 @@ Python.") (define-public python-biom-format (package (name "python-biom-format") - (version "2.1.7") + (version "2.1.10") (source (origin (method git-fetch) @@ -1025,18 +1029,21 @@ Python.") (file-name (git-file-name name version)) (sha256 (base32 - "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")) + "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8")) (modules '((guix build utils))) - (snippet '(begin - ;; Delete generated C files. - (for-each delete-file (find-files "." "\\.c")) - #t)))) + ;; Delete generated C files. + (snippet + '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-cython - (lambda _ (setenv "USE_CYTHON" "1") #t)) + (lambda _ (setenv "USE_CYTHON" "1"))) + (add-after 'unpack 'relax + (lambda _ + (substitute* "setup.py" + (("pytest < 5.3.4") "pytest")))) (add-after 'unpack 'disable-broken-tests (lambda _ (substitute* "biom/tests/test_cli/test_validate_table.py" @@ -1048,24 +1055,22 @@ Python.") (("^(.+)def test_from_hdf5_issue_731" m indent) (string-append indent "@npt.dec.skipif(True, msg='Guix')\n" - m))) - #t)) + m))))) + (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (for-each (lambda (file) (chmod file #o644)) - (find-files out "\\.gz")) - #t)))))) + (find-files out "\\.gz")))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) + `(("python-anndata" ,python-anndata) + ("python-numpy" ,python-numpy) ("python-scipy" ,python-scipy) ("python-flake8" ,python-flake8) ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py) - ;; FIXME: Upgrade to pandas 1.0 when - ;; https://github.com/biocore/biom-format/issues/837 is resolved. - ("python-pandas" ,python-pandas-0.25))) + ("python-pandas" ,python-pandas))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) @@ -1078,23 +1083,7 @@ Python.") representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-biom-format)))))) - -(define-public python2-biom-format - (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) - (package - (inherit base) - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - ;; Do not require the unmaintained pyqi library. - (add-after 'unpack 'remove-pyqi - (lambda _ - (substitute* "setup.py" - (("install_requires.append\\(\"pyqi\"\\)") "pass")) - #t))))))))) + (license license:bsd-3))) (define-public python-pairtools (package @@ -2690,77 +2679,6 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") (home-page "https://sourceforge.net/projects/codingquarry/") (license license:gpl3+))) -(define-public couger - (package - (name "couger") - (version "1.8.2") - (source (origin - (method url-fetch) - (uri (string-append - "http://couger.oit.duke.edu/static/assets/COUGER" - version ".zip")) - (sha256 - (base32 - "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (copy-recursively "src" (string-append out "/src")) - (mkdir bin) - ;; Add "src" directory to module lookup path. - (substitute* "couger" - (("from argparse") - (string-append "import sys\nsys.path.append(\"" - out "\")\nfrom argparse"))) - (install-file "couger" bin)) - #t)) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'couger' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/couger") - `("GUIX_PYTHONPATH" ":" prefix (,path)))) - #t))))) - (inputs - `(("python" ,python-2) - ("python2-pillow" ,python2-pillow) - ("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-matplotlib" ,python2-matplotlib))) - (propagated-inputs - `(("r-minimal" ,r-minimal) - ("libsvm" ,libsvm) - ("randomjungle" ,randomjungle))) - (native-inputs - `(("unzip" ,unzip))) - (home-page "http://couger.oit.duke.edu") - (synopsis "Identify co-factors in sets of genomic regions") - (description - "COUGER can be applied to any two sets of genomic regions bound by -paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify -putative co-factors that provide specificity to each TF. The framework -determines the genomic targets uniquely-bound by each TF, and identifies a -small set of co-factors that best explain the in vivo binding differences -between the two TFs. - -COUGER uses classification algorithms (support vector machines and random -forests) with features that reflect the DNA binding specificities of putative -co-factors. The features are generated either from high-throughput TF-DNA -binding data (from protein binding microarray experiments), or from large -collections of DNA motifs.") - (license license:gpl3+))) - (define-public clustal-omega (package (name "clustal-omega") @@ -5070,23 +4988,26 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (("# libraries = z,bz2") "libraries = z,bz2") (("include:third-party/zlib:third-party/bzip2") - "include:")) - #t)))) + "include:")))))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-cc - (lambda _ (setenv "CC" "gcc") #t)) - + (lambda _ (setenv "CC" "gcc"))) + (add-after 'unpack 'python-3.8-compatibility + (lambda _ + ;; Python 3.8 removed time.clock(). + (substitute* "sandbox/sweep-reads.py" + (("time\\.clock") + "time.process_time")))) (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) ;; Make sure .gz files are writable so that the ;; 'reset-gzip-timestamps' phase can do its work. (let ((out (assoc-ref outputs "out"))) (for-each make-file-writable - (find-files out "\\.gz$")) - #t)))))) + (find-files out "\\.gz$")))))))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) @@ -7764,12 +7685,27 @@ single cell ATAC-seq sequencing data.") (base32 "0bjzamdw2lcfhlbzc0vdva87c3wwnij8jsvnrpx4wyyxvpcz13m5")))) (properties `((upstream-name . "umi4cPackage"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-references + (lambda _ + (substitute* "inst/conf/paths.conf" + (("TG3C\\.bowtie2_bin=.*") + (string-append "TG3C.bowtie2_bin=" + (which "bowtie2") "\n"))) + (substitute* "inst/perl/map3c/TG3C/import3C.pl" + (("\"perl") + (string-append "\"" (which "perl"))))))))) + (inputs + `(("perl" ,perl) + ("bowtie" ,bowtie))) (propagated-inputs `(("r-misha" ,r-misha) ("r-zoo" ,r-zoo))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tanaylab/umi4cpackage") - (synopsis "Processing and analysis of UMI-4C contact profiles.") + (synopsis "Processing and analysis of UMI-4C contact profiles") (description "This is a package that lets you process UMI-4C data from scratch to produce nice plots.") (license license:expat)))) @@ -8134,29 +8070,27 @@ Needleman-Wunsch).") (define-public pardre (package (name "pardre") - ;; The source of 1.1.5 changed in place, so we append "-1" to the version. - (version "1.1.5-1") + (version "2.2.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" - "1.1.5" ".tar.gz")) + version ".tar.gz")) (sha256 (base32 - "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) + "105s4f8zs8hh0sc32r9p725n7idza9cj5jvp5z1m5pljjhgk3if5")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no tests included + `(#:tests? #f ; tests require "prove" #:phases (modify-phases %standard-phases (delete 'configure) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "ParDRe" bin) - #t)))))) + (install-file "ParDRe" bin))))))) (inputs - `(("openmpi" ,openmpi) + `(("openmpi-c++" ,openmpi-c++) ("zlib" ,zlib))) (synopsis "Parallel tool to remove duplicate DNA reads") (description @@ -9388,7 +9322,7 @@ programs for inferring phylogenies (evolutionary trees).") (define-public imp (package (name "imp") - (version "2.13.0") + (version "2.15.0") (source (origin (method url-fetch) @@ -9396,7 +9330,7 @@ programs for inferring phylogenies (evolutionary trees).") version "/download/imp-" version ".tar.gz")) (sha256 (base32 - "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj")))) + "05hsrnkpkajppa3f45x4qsarnkj616hlby749zxg4is3bv4i6b5y")))) (build-system cmake-build-system) (arguments `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used @@ -9409,7 +9343,9 @@ programs for inferring phylogenies (evolutionary trees).") "IMP.parallel-test_sge.py" ;fail in build container ;; The following test fails non-reproducibly on ;; an inexact numbers assertion. - "IMP.em-medium_test_local_fitting.py"))) + "IMP.em-medium_test_local_fitting.py" + ;; The following test fails for unknown reasons + "IMP.foxs-add-missing-residues.py"))) (list (string-append "-DCMAKE_CTEST_ARGUMENTS=" @@ -10321,6 +10257,46 @@ graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) +(define-public python-biothings-client + (package + (name "python-biothings-client") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "biothings_client" version)) + (sha256 + (base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4")))) + (build-system python-build-system) + (arguments `(#:tests? #false)) ; require internet access + (propagated-inputs `(("python-requests" ,python-requests))) + (home-page "https://github.com/biothings/biothings_client.py") + (synopsis "Python client for BioThings API services") + (description "This package provides a Python client for BioThings +API services.") + (license license:bsd-3))) + +(define-public python-mygene + (package + (name "python-mygene") + (version "3.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mygene" version)) + (sha256 + (base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7")))) + (build-system python-build-system) + (propagated-inputs + `(("python-biothings-client" ,python-biothings-client))) + (home-page "https://github.com/biothings/mygene.py") + (synopsis "Python Client for MyGene.Info services.") + (description "MyGene.Info provides simple-to-use REST web services +to query/retrieve gene annotation data. It's designed with simplicity +and performance emphasized. Mygene is a Python wrapper to access +MyGene.Info services.") + (license license:bsd-3))) + ;; We cannot use the latest commit because it requires Java 9. (define-public java-forester (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") @@ -11181,7 +11157,7 @@ based methods.") (define-public pigx-sars-cov2-ww (package (name "pigx-sars-cov2-ww") - (version "0.0.3") + (version "0.0.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" @@ -11189,7 +11165,7 @@ based methods.") "/pigx_sars-cov2-ww-" version ".tar.gz")) (sha256 (base32 - "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw")) + "0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs")) (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch")))) (build-system gnu-build-system) (arguments @@ -11203,9 +11179,13 @@ based methods.") ("autoconf" ,autoconf))) (inputs `(("bash-minimal" ,bash-minimal) + ("bbmap" ,bbmap) + ("bedtools" ,bedtools) ("bwa" ,bwa) ("ensembl-vep" ,ensembl-vep) + ("fastp" ,fastp) ("fastqc" ,fastqc) + ("ivar" ,ivar) ("kraken2" ,kraken2) ("krona-tools" ,krona-tools) ("lofreq" ,lofreq) @@ -11221,6 +11201,7 @@ based methods.") ("r-minimal" ,r-minimal) ("r-plotly" ,r-plotly) ("r-qpcr" ,r-qpcr) + ("r-r-utils" ,r-r-utils) ("r-reshape2" ,r-reshape2) ("r-rmarkdown" ,r-rmarkdown) ("r-stringr" ,r-stringr) @@ -11393,7 +11374,7 @@ version does count multisplits.") (define-public minimap2 (package (name "minimap2") - (version "2.18") + (version "2.23") (source (origin (method url-fetch) @@ -11402,7 +11383,7 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs")))) + "00ngbz1swcgxk5apx9dz5xkh1z8abdpysx5lc7w8fbrfxp41w0j0")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none @@ -13824,10 +13805,47 @@ vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using @code{ggplot2}.") (license license:expat))) +(define-public vbz-compression + (package + (name "vbz-compression") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nanoporetech/vbz_compression/") + (commit (string-append "v" version)) + ;; We include the streamvbyte sources + (recursive? #true))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c6wsrnw03vsc5cfp2rdakly5xy55m9chjmy6v685yapdwirdky0")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + '("-DENABLE_CONAN=OFF" + ;; Python things aren't even installed, so we might as well + ;; disable building them. + "-DENABLE_PYTHON=OFF"))) + (inputs + `(;("hdf5" ,hdf5-1.10) + ("zstd" ,zstd "lib"))) + (native-inputs + `(("googlebenchmark" ,googlebenchmark))) + (home-page "https://github.com/nanoporetech/vbz_compression/") + (synopsis "VBZ compression plugin for nanopore signal data") + (description + "VBZ Compression uses variable byte integer encoding to compress +nanopore signal data. The performance of VBZ is achieved by taking +advantage of the properties of the raw signal and therefore is most +effective when applied to the signal dataset.") + (license license:mpl2.0))) + (define-public python-ont-fast5-api (package (name "python-ont-fast5-api") - (version "1.4.4") + (version "4.0.0") (source (origin (method git-fetch) @@ -13837,12 +13855,27 @@ are generated using @code{ggplot2}.") (file-name (git-file-name name version)) (sha256 (base32 - "03cbq4zbbwhll8ml2m9k8sa31mirsvcbjkrq1yna0kkzz9fad5fm")))) + "01hj4751j424lzic2sc4bz1f8w7i7fpkjpy3rgghdyl5lyfyb4s4")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "ont_fast5_api/vbz_plugin")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-plugin + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "ont_fast5_api/vbz_plugin/") + (install-file (string-append + (assoc-ref inputs "vbz-compression") + "/hdf5/lib/plugin/libvbz_hdf_plugin.so") + "ont_fast5_api/vbz_plugin/")))))) + (inputs + `(("vbz-compression" ,vbz-compression))) (propagated-inputs `(("python-numpy" ,python-numpy) - ("python-six" ,python-six) ("python-h5py" ,python-h5py) + ("python-packaging" ,python-packaging) ("python-progressbar33" ,python-progressbar33))) (home-page "https://github.com/nanoporetech/ont_fast5_api") (synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format") @@ -14814,6 +14847,7 @@ usually ignored by other methods or only used for filtering.") (base32 "044xa0hm3b8fga64csrdx05ih8w7kwmvcdrdrhkg8j11ml4bi4xv")))) (build-system gnu-build-system) + (arguments `(#:parallel-tests? #false)) ; not supported (inputs `(("htslib" ,htslib) ("zlib" ,zlib))) |