diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 450 |
1 files changed, 31 insertions, 419 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 067fb5cb86..b82ec38157 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -350,40 +350,6 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) -(define-public bcftools-1.12 - (package/inherit bcftools - (version "1.12") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/samtools/bcftools/" - "releases/download/" - version "/bcftools-" version ".tar.bz2")) - (sha256 - (base32 - "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks")) - (modules '((guix build utils))) - (snippet '(begin - ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.12"))))) - (native-inputs (list htslib-1.12 perl)))) - -(define-public bcftools-1.10 - (package/inherit bcftools - (version "1.10") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/samtools/bcftools/" - "releases/download/" - version "/bcftools-" version ".tar.bz2")) - (sha256 - (base32 - "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra")) - (modules '((guix build utils))) - (snippet '(begin - ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.10"))))) - (native-inputs (list htslib-1.10 perl)))) - (define-public bedops (package (name "bedops") @@ -2900,8 +2866,8 @@ biological activities from omics data within a unified framework.") (license license:bsd-3))) ;; See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200> -(define-public python-decoupler-py - (deprecated-package "python-decoupler-py" python-decoupler)) +(define-deprecated-package python-decoupler-py + python-decoupler) (define-public python-demuxem (package @@ -2964,7 +2930,7 @@ demultiplexing step.") (list python-anndata python-ipywidgets python-leidenalg - python-vtraag-louvain + python-louvain-igraph python-matplotlib python-numpy python-pandas @@ -6027,8 +5993,8 @@ subgroups.") (description "muon is a multimodal omics Python framework.") (license license:bsd-3))) -(define-public python-pyega3 - (deprecated-package "python-pyega3" python-ega-download-client)) +(define-deprecated-package python-pyega3 + python-ega-download-client) (define-public python-pysam (package @@ -6121,79 +6087,6 @@ also includes an interface for tabix.") UCSC genome browser.") (license license:artistic2.0))) -(define-public python-plastid - (package - (name "python-plastid") - (version "0.6.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/joshuagryphon/plastid") - (commit "d97f239d73b3a7c2eff46f71928b777431891f90"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0iccpywlpf1ws46279z9rl0l29pil0rj0g2j5nvqq7jfbnq581cf")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list "plastid/test" - ;; These four failures look like errors in the test wrapper - ;; class. - "-k" (string-append "not test_chrom_sizes" - " and not test_no_crash_if_file_not_exist" - " and not test_fiveprime_variable" - " and not test_fiveprime_variable_from_file")) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'unpack-test-data - (lambda* (#:key inputs #:allow-other-keys) - (invoke "tar" "-C" "plastid/test" - "-xf" (assoc-ref inputs "test-data")) - ;; This one requires bowtie-build - (delete-file "plastid/test/functional/test_crossmap.py"))) - (add-after 'unpack 'patch-for-python-3.10 - (lambda _ - ;; Some classes were moved from collections to collections.abc - ;; in Python 3.10. - (substitute* "plastid/readers/bigbed.pyx" - ((", Iterable") - "\nfrom collections.abc import Iterable")))) - (add-before 'check 'build-extensions - (lambda _ - ;; Cython extensions have to be built before running the tests. - (invoke "python3" "setup.py" "build_ext" "--inplace")))))) - (propagated-inputs - (list python-numpy - python-scipy - python-pandas - python-pysam - python-matplotlib - python-biopython - python-twobitreader - python-termcolor)) - (inputs - (list openssl)) - (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-setuptools" ,python-setuptools) - ("python-wheel" ,python-wheel) - ("test-data" - ,(origin - (method url-fetch) - (uri "https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=1") - (file-name "plastid-test-data-2022-05-04.tar.bz2") - (sha256 - (base32 "1szsji06m2r21flnvxg84jnj5zmlk6z10c9651v9ag71nxj9rbzn")))))) - (home-page "https://github.com/joshuagryphon/plastid") - (synopsis "Python library for genomic analysis") - (description - "plastid is a Python library for genomic analysis – in particular, -high-throughput sequencing data – with an emphasis on simplicity.") - (license license:bsd-3))) - (define-public tetoolkit (package (name "tetoolkit") @@ -9706,48 +9599,6 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) -(define-public htslib-1.19 - (package - (inherit htslib) - (version "1.19") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/samtools/htslib/releases/download/" - version "/htslib-" version ".tar.bz2")) - (sha256 - (base32 - "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7")) - (snippet - #~(begin - (use-modules (guix build utils)) - (delete-file-recursively "htscodecs"))))) - (build-system gnu-build-system) - ;; Let htslib translate "gs://" and "s3://" to regular https links with - ;; "--enable-gcs" and "--enable-s3". For these options to work, we also - ;; need to set "--enable-libcurl". - (arguments - `(#:configure-flags '("--enable-gcs" - "--enable-libcurl" - "--enable-s3" - "--with-external-htscodecs"))) - (inputs - (list bzip2 curl openssl xz)) - ;; This is referred to in the pkg-config file as a required library. - (propagated-inputs - (list htscodecs zlib)) - (native-inputs - (list perl)) - (home-page "https://www.htslib.org") - (synopsis "C library for reading/writing high-throughput sequencing data") - (description - "HTSlib is a C library for reading/writing high-throughput sequencing -data. It also provides the @command{bgzip}, @command{htsfile}, and -@command{tabix} utilities.") - ;; Files under cram/ are released under the modified BSD license; - ;; the rest is released under the Expat license - (license (list license:expat license:bsd-3)))) - (define-public htslib-1.14 (package/inherit htslib (version "1.14") @@ -9767,37 +9618,6 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (modify-inputs (package-propagated-inputs htslib) (delete "htscodecs"))))) -(define-public htslib-1.12 - (package/inherit htslib - (version "1.12") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/samtools/htslib/releases/download/" - version "/htslib-" version ".tar.bz2")) - (sha256 - (base32 - "1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012")))) - (arguments - (substitute-keyword-arguments (package-arguments htslib) - ((#:configure-flags cf #~'()) - #~(delete "--with-external-htscodecs" #$cf)))) - (propagated-inputs - (modify-inputs (package-propagated-inputs htslib) - (delete "htscodecs"))))) - -(define-public htslib-1.10 - (package/inherit htslib - (version "1.10") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/samtools/htslib/releases/download/" - version "/htslib-" version ".tar.bz2")) - (sha256 - (base32 - "0wm9ay7qgypj3mwx9zl1mrpnr36298b1aj5vx69l4k7bzbclvr3s")))))) - (define-public htslib-1.9 (package/inherit htslib (version "1.9") @@ -9823,41 +9643,6 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (base32 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) -(define htslib-for-samtools-1.2 - (package/inherit htslib - (version "1.2.1") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/samtools/htslib/releases/download/" - version "/htslib-" version ".tar.bz2")) - (sha256 - (base32 - "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - (("/bin/bash") (which "bash")))))))) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("perl" ,perl))))) - -(define htslib-for-stringtie - (package - (inherit htslib-1.12) - (source (origin - (inherit (package-source htslib-1.12)) - (patches - (search-patches "htslib-for-stringtie.patch")))) - (arguments - `(#:configure-flags '("--with-libdeflate"))) - (inputs - (list bzip2 libdeflate openssl)))) - (define-public idr (package (name "idr") @@ -11309,145 +11094,6 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) -(define-public samtools-1.14 - (package/inherit samtools - (version "1.14") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/samtools/samtools/" - version "/samtools-" version ".tar.bz2")) - (sha256 - (base32 - "0x3xdda78ac5vx66b3jdsv9sfhyz4npl4znl1zbaf3lbm6xdlhck")) - (modules '((guix build utils))) - (snippet '(begin - ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.14"))))) - (native-inputs (list pkg-config)) - (inputs - (list htslib-1.14 ncurses perl python zlib)))) - -(define-public samtools-1.12 - (package/inherit samtools - (version "1.12") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/samtools/samtools/" - version "/samtools-" version ".tar.bz2")) - (sha256 - (base32 - "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd")) - (modules '((guix build utils))) - (snippet '(begin - ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.12"))))) - (arguments - (substitute-keyword-arguments (package-arguments samtools) - ((#:modules _ #f) - '((ice-9 ftw) - (ice-9 regex) - (guix build gnu-build-system) - (guix build utils))) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'install 'install-library - (lambda* (#:key outputs #:allow-other-keys) - (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (install-file "libbam.a" lib)))) - (add-after 'install 'install-headers - (lambda* (#:key outputs #:allow-other-keys) - (let ((include (string-append (assoc-ref outputs "out") - "/include/samtools/"))) - (for-each (lambda (file) - (install-file file include)) - (scandir "." (lambda (name) - (string-match "\\.h$" name))))))))))) - (native-inputs (list pkg-config)) - (inputs - (list htslib-1.12 ncurses perl python zlib)))) - -(define-public samtools-1.10 - (package (inherit samtools) - (name "samtools") - (version "1.10") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/samtools/samtools/" - version "/samtools-" version ".tar.bz2")) - (sha256 - (base32 - "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv")) - (modules '((guix build utils))) - (snippet '(begin - ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.10") - #t)))) - (inputs - (list htslib-1.10 ncurses perl python zlib)))) - -(define-public samtools-1.2 - (package (inherit samtools) - (name "samtools") - (version "1.2") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/samtools/samtools/" - version "/samtools-" version ".tar.bz2")) - (sha256 - (base32 - "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2")) - (modules '((guix build utils))) - (snippet - ;; Delete bundled htslib and Windows binaries - '(for-each delete-file-recursively (list "win32" "htslib-1.2.1"))))) - (arguments - `(#:make-flags - ,#~(list (string-append "prefix=" #$output) - (string-append "BGZIP=" - #$(this-package-input "htslib") - "/bin/bgzip") - (string-append "HTSLIB=" - #$(this-package-input "htslib") - "/lib/libhts.so") - (string-append "HTSDIR=" - #$(this-package-input "htslib") - "/include")) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-makefile-curses - (lambda _ - (substitute* "Makefile" - (("-lcurses") "-lncurses") - (("include \\$\\(HTSDIR.*") "")))) - (add-after 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") (which "bash")) - ;; There are two failing tests upstream relating to the "stats" - ;; subcommand in test_usage_subcommand ("did not have Usage" - ;; and "usage did not mention samtools stats"), so we disable - ;; them. - (("(test_usage_subcommand\\(.*\\);)" cmd) - (string-append "unless ($subcommand eq 'stats') {" cmd "};"))) - ;; This test fails because the grep output doesn't look as - ;; expected; it is correct, though. - (substitute* "test/mpileup/mpileup.reg" - (("P 52.out.*") "")))) - (delete 'configure)))) - (native-inputs - (list grep gawk pkg-config)) - (inputs - (list htslib-for-samtools-1.2 ncurses perl python zlib)))) - (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input ;; and output formats differ greatly from that used and produced by samtools @@ -12794,14 +12440,14 @@ against local background noises.") (define-public stringtie (package (name "stringtie") - (version "2.2.0") + (version "3.0.2") (source (origin (method url-fetch) (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" "stringtie-" version ".tar.gz")) (sha256 (base32 - "08w3ish4y9kf9acp7k38iwi8ixa6j51m6qyf0vvfj7yz78a3ai3x")) + "1mrqcvnhxbidyhf521naywb5ci579160ydqnl5kb4hqjqvm01mn2")) ;; This package bundles an annoying amount of third party source ;; code. (modules '((guix build utils))) @@ -12827,7 +12473,7 @@ against local background noises.") (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (install-file "stringtie" bin))))))) (inputs - (list bzip2 htslib-for-stringtie libdeflate zlib)) + (list bzip2 htslib libdeflate zlib)) (home-page "https://ccb.jhu.edu/software/stringtie/") (synopsis "Transcript assembly and quantification for RNA-Seq data") (description @@ -17461,8 +17107,8 @@ lowly expressed transcripts.") mapped paired-end sequencing reads.") (license license:gpl3+))) -(define-public fanc - (deprecated-package "fanc" python-fanc)) +(define-deprecated-package fanc + python-fanc) (define-public python-genomic-regions (package @@ -18714,8 +18360,8 @@ report will provide an intuitive visual overview about the development of variant abundance over time and location.") (license license:gpl3+))) -(define-public pigx-sars-cov2-ww - (deprecated-package "pigx-sars-cov2-ww" pigx-sars-cov-2)) +(define-deprecated-package pigx-sars-cov2-ww + pigx-sars-cov-2) (define-public pigx (package @@ -20178,26 +19824,31 @@ set.") (define-public instrain (package (name "instrain") - (version "1.9.0") + ;; Git repository does not tag releases, use the latest commit from master + ;; branch. + (properties '((commit . "6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3") + (revision . "0"))) + (version (git-version "1.10.0" + (assoc-ref properties 'revision) + (assoc-ref properties 'commit))) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/MrOlm/instrain") - ;; There are no tags. - (commit "168f3f777b45139a9f6099f68974105b45e2d8ba"))) + (url "https://github.com/MrOlm/instrain") + (commit (assoc-ref properties 'commit)))) (file-name (git-file-name name version)) (sha256 - (base32 - "1wc69ggyiacm1slb678239lqmf1g5dlb4alwsbp14gi6393gj9fg")))) + (base32 "1njsxjf3248121yw3q1ig6asf6b3wa5fgjfyc6dkgk6nd4ih8wni")))) (build-system pyproject-build-system) (arguments (list ;; Tests assume that test files exist (they don't) and are located in - ;; the developer's home directory. + ;; the developer's home directory, see: + ;; <https://github.com/MrOlm/inStrain/issues/218>. #:tests? #false #:phases - '(modify-phases %standard-phases + #~(modify-phases %standard-phases (add-after 'unpack 'patch-relative-imports (lambda _ (substitute* (find-files "test/tests" "test_.*\\.py") @@ -20208,7 +19859,11 @@ set.") (("from s3_utils") "from .s3_utils") (("from job_utils") - "from .job_utils"))))))) + "from .job_utils")))) + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + ((".*pytest.*") ""))))))) (propagated-inputs (list python-biopython-1.73 python-h5py @@ -20222,10 +19877,7 @@ set.") python-seaborn python-tqdm)) (native-inputs - (list python-boto3 - python-pytest - python-setuptools - python-wheel)) + (list python-setuptools)) (home-page "https://github.com/MrOlm/inStrain") (synopsis "Calculation of strain-level metrics") (description @@ -21511,46 +21163,6 @@ filtered first. If no annotation entry remains, the entire variant is deleted.") (license license:expat))) -(define-public python-velocyto - (package - (name "python-velocyto") - (version "0.17.17") - (source - (origin - (method url-fetch) - (uri (pypi-uri "velocyto" version)) - (sha256 - (base32 "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs")) - (modules '((guix build utils))) - ;; Delete generated C files. - (snippet '(for-each delete-file - (find-files "." "\\.c"))))) - (build-system pyproject-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - ;; Numba needs a writable dir to cache functions. - (add-before 'check 'set-numba-cache-dir - (lambda _ - (setenv "NUMBA_CACHE_DIR" "/tmp")))))) - (native-inputs (list python-joblib python-setuptools python-wheel)) - (propagated-inputs (list python-click - python-cython - python-h5py - python-loompy - python-matplotlib - python-numba - python-numpy - python-pandas - python-pysam - python-scikit-learn - python-scipy)) - (home-page "https://github.com/velocyto-team/velocyto.py") - (synopsis "RNA velocity analysis for single cell RNA-seq data") - (description - "Velocyto is a library for the analysis of RNA velocity. Velocyto -includes a command line tool and an analysis pipeline.") - (license license:bsd-2))) - (define-public arriba (package (name "arriba") |