diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 473 |
1 files changed, 433 insertions, 40 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 054776da5b..ba8c47451f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3985,26 +3985,44 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.12.3") + (version "2.0.2") + ;; Sources on pypi do not include everything needed to run the tests. (source (origin - (method url-fetch) - (uri (pypi-uri "HTSeq" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/htseq/htseq") + (commit (string-append "release_" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b")))) + "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19")))) (build-system python-build-system) - (native-inputs - (list python-cython)) - ;; Numpy needs to be propagated when htseq is used as a Python library. + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Avoid rebuilding the extension. Everything is built during the + ;; 'install phase anyway. + (delete 'build) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) (propagated-inputs - (list python-numpy)) - (inputs - (list python-pysam python-matplotlib)) - (home-page "https://htseq.readthedocs.io/") - (synopsis "Analysing high-throughput sequencing data with Python") + (list python-matplotlib + python-numpy + python-pysam)) + (native-inputs + (list python-cython + python-pandas + python-pytest + python-scipy + swig)) + (home-page "https://github.com/htseq") + (synopsis "Framework for analyzing high-throughput sequencing data") (description - "HTSeq is a Python package that provides infrastructure to process data -from high-throughput sequencing assays.") + "This package provides a framework to process and analyze data from +high-throughput sequencing (HTS) assays") (license license:gpl3+))) (define-public java-htsjdk @@ -6276,36 +6294,37 @@ subsequent visualization, annotation and storage of results.") (base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0")))) (build-system gnu-build-system) (arguments - `(#:make-flags - ,#~(list "BLASFLAGS=-llapack -lopenblas" - (string-append "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" - " -I" (search-input-directory - %build-inputs "include/simde")) - "ZLIB=-lz" - "BIN=plink prettify" - (string-append "CC=" #$(cc-for-target)) - (string-append "PREFIX=" #$output) - "DESTDIR=") - #:phases - (modify-phases %standard-phases + (list + #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files + #:make-flags + #~(list "BLASFLAGS=-llapack -lopenblas" + "NO_SSE42=1" + "NO_AVX2=1" + "STATIC_ZSTD=" + (string-append "CC=" #$(cc-for-target)) + (string-append "PREFIX=" #$output) + "DESTDIR=") + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "1.9"))) - (delete 'configure) ; no "configure" script + (lambda _ (chdir "2.0/build_dynamic"))) + (delete 'configure) ; no "configure" script (replace 'check (lambda* (#:key tests? inputs #:allow-other-keys) (when tests? - (symlink "plink" "plink19") - (symlink (search-input-file inputs "/bin/plink") "plink107") (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) - (with-directory-excursion "tests" - ;; The model test fails because of a 0.0001 difference. - (substitute* "tests.py" - (("diff -q test1.model test2.model") - "echo yes")) - (invoke "bash" "test_setup.sh") - (invoke "python3" "tests.py")))))))) + (with-directory-excursion "../Tests" + (substitute* "run_tests.sh" + (("^./run_tests" m) + (string-append (which "bash") " " m))) + (invoke "bash" "run_tests.sh"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "plink2" + (string-append + (assoc-ref outputs "out") "/bin"))))))) (inputs - (list lapack openblas zlib)) + (list lapack openblas zlib `(,zstd "lib"))) (native-inputs (list diffutils plink python simde)) ; for tests (home-page "https://www.cog-genomics.org/plink/") @@ -6430,6 +6449,86 @@ Values such as sequence name, sequence description, sequence quality and the sequence itself can be retrieved from these databases.") (license license:bsd-3))) +(define-public python-taggd + (package + (name "python-taggd") + (version "0.3.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SpatialTranscriptomicsResearch/taggd") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0j19ah81z7aqrdljah9hyarp91gvgbk63pz6fz3pdpksy1yqyi6k")) + (modules '((guix build utils))) + (snippet + '(for-each delete-file + (find-files "taggd" "\\.c$"))))) + (build-system python-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-broken-tests + (lambda _ + (substitute* "tests/taggd_demultiplex_test.py" + (("def test_normal_bam_run") + "def _disabled_test_normal_bam_run"))))))) + (propagated-inputs + (list python-numpy python-pysam python-setuptools)) + (native-inputs + (list python-cython)) + (home-page "https://github.com/SpatialTranscriptomicsResearch/taggd") + (synopsis "Genetic barcode demultiplexing") + (description "This package provides TagGD barcode demultiplexing utilities +for Spatial Transcriptomics data.") + (license license:bsd-3))) + +(define-public stpipeline + (package + (name "stpipeline") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "stpipeline" version)) + (sha256 + (base32 + "0har2g42fvaqpiz66lincy86aj1hvwzds26kxhxfamvyvv4721wk")))) + (build-system python-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "requirements.txt" + (("argparse.*") ""))))))) + (propagated-inputs + (list htseq + python-cython + python-invoke + python-numpy + python-pandas + python-pympler + python-pysam + python-regex + python-scikit-learn + python-scipy + python-seaborn + python-setuptools + python-sqlitedict + python-taggd + samtools + star)) + (home-page "https://github.com/SpatialTranscriptomicsResearch/st_pipeline") + (synopsis "Pipeline for spatial mapping of unique transcripts") + (description + "This package provides an automated pipeline for spatial mapping of +unique transcripts.") + (license license:expat))) + (define-public sra-tools (package (name "sra-tools") @@ -11292,13 +11391,13 @@ cases include: (define-public python-mappy (package (name "python-mappy") - (version "2.18") + (version "2.24") (source (origin (method url-fetch) (uri (pypi-uri "mappy" version)) (sha256 (base32 - "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq")))) + "1ycszza87p9qvx8mis9v1hry0ac465x1xcxbsn1k45qlxxrzp8im")))) (build-system python-build-system) (native-inputs (list python-cython)) @@ -16097,6 +16196,32 @@ control samples and applying quantile normalization on all markers of interest.") (license license:gpl2+)))) +(define-public r-kbet + (let ((commit "f35171dfb04c7951b8a09ac778faf7424c4b6bc0") + (revision "1")) + (package + (name "r-kbet") + (version (git-version "0.99.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/theislab/kBET") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r91prl2kki3zk694vhlmxdlqh0ixlhs8jfcqw6wc7cdsa0nv67k")))) + (properties `((upstream-name . "kBET"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster r-fnn r-ggplot2 r-mass r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/theislab/kBET") + (synopsis "k-nearest neighbour batch effect test") + (description + "This tool detects batch effects in high-dimensional data based on chi^2-test.") + ;; Any version of the GPL + (license license:gpl3+)))) + (define-public ccwl (package (name "ccwl") @@ -16330,3 +16455,271 @@ alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.") (home-page "https://github.com/ekg/wfmash") (license license:expat))) + +(define-public flair + (package + (name "flair") + (version "1.6.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BrooksLabUCSC/flair") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "106swb2q7l20ki58fca1hg95q5f79bgp9gjb0clr2243ycrzyxf8")))) + (build-system python-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + #~(modify-phases %standard-phases + ;; TODO: implement as a feature of python-build-system (PEP-621, + ;; PEP-631, PEP-660) + (replace 'build + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda _ + (apply invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output + (find-files "dist" "\\.whl$"))))))) + (propagated-inputs + (list python-mappy + python-ncls + python-pybedtools + python-pysam + python-tqdm)) + (native-inputs + (list python-pypa-build python-setuptools)) + (home-page "https://flair.readthedocs.io/en/latest/") + (synopsis "Full-length alternative isoform analysis of RNA") + (description "This package implements FLAIR (Full-Length Alternative +Isoform analysis of RNA) for the correction, isoform definition, and +alternative splicing analysis of noisy reads. FLAIR has primarily been used +for nanopore cDNA, native RNA, and PacBio sequencing reads.") + (license license:bsd-3))) + +(define-public go-github-com-biogo-graph + (package + (name "go-github-com-biogo-graph") + (version "0.0.0-20150317020928-057c1989faed") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biogo/graph") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1kpzs5dfd5dsk4mg1g2qjz1prqd84ixhrcxxnf90hq25vxcnk7lh")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/biogo/graph" + #:tests? #false)) ;TODO: one of 13 tests fails for unknown reasons + (propagated-inputs + (list go-gopkg-in-check-v1)) + (home-page "https://github.com/biogo/graph") + (synopsis "Undirected graph analysis for biogo") + (description "The package @code{graph} implements graph manipulation +functions.") + (license license:bsd-3))) + +(define-public go-github-com-biogo-store-interval + (package + (name "go-github-com-biogo-store-interval") + (version "0.0.0-20201120204734-aad293a2328f") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biogo/store") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0skizrp1j6vgbl0g1kmh73picagqlvwckaqs0gkl6rai5lckxj8a")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/biogo/store/interval" + #:unpack-path "github.com/biogo/store")) + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github-com-kr-pretty)) + (home-page "https://github.com/biogo/store") + (synopsis "Interval store type for biogo") + (description + "The @code{store} package provides a number of data store types that are +useful for bioinformatic analysis.") + (license license:bsd-3))) + +(define-public go-github-com-biogo-store-kdtree + (package + (inherit go-github-com-biogo-store-interval) + (name "go-github-com-biogo-store-kdtree") + (arguments + '(#:import-path "github.com/biogo/store/kdtree" + #:unpack-path "github.com/biogo/store")) + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github-com-kr-pretty)) + (synopsis "kdtree store type for biogo"))) + +(define-public go-github-com-biogo-store-llrb + (package + (inherit go-github-com-biogo-store-interval) + (name "go-github-com-biogo-store-llrb") + (arguments + '(#:import-path "github.com/biogo/store/llrb" + #:unpack-path "github.com/biogo/store")) + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github-com-kr-pretty)) + (synopsis "LLRB store for biogo"))) + +(define-public go-github-com-biogo-store-step + (package + (inherit go-github-com-biogo-store-interval) + (name "go-github-com-biogo-store-step") + (arguments + '(#:import-path "github.com/biogo/store/step" + #:unpack-path "github.com/biogo/store")) + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github-com-kr-pretty)) + (synopsis "Step store for biogo"))) + +(define-public go-github-com-biogo-hts-bam + (package + (name "go-github-com-biogo-hts-bam") + (version "1.4.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biogo/hts") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "013ga6ilc4m3hyfr3yyiva9g4vs81afhj73v2sy7r75b5zxw7lx1")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/biogo/hts/bam" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (home-page "https://github.com/biogo/hts") + (synopsis "HTS BAM module for biogo") + (description "This package provides tools for handling BAM files.") + (license license:bsd-3))) + +(define-public go-github-com-biogo-hts-sam + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-sam") + (arguments + '(#:import-path "github.com/biogo/hts/sam" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (synopsis "HTS SAM module for biogo") + (description "This package provides tools for handling SAM files."))) + +(define-public go-github-com-biogo-hts-tabix + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-tabix") + (arguments + '(#:import-path "github.com/biogo/hts/tabix" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (synopsis "HTS Tabix module for biogo") + (description "This package provides tools for handling Tabix files."))) + +(define-public go-github-com-biogo-hts-bgzf + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-bgzf") + (arguments + '(#:import-path "github.com/biogo/hts/bgzf" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (synopsis "HTS bgzf module for biogo") + (description "This package provides tools for handling bgzf files."))) + +(define-public go-github-com-biogo-hts-cram + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-cram") + (arguments + '(#:import-path "github.com/biogo/hts/cram" + #:unpack-path "github.com/biogo/hts" + #:tests? #false)) ;require network access + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github.com-ulikunitz-xz + go-github-com-kortschak-utter)) + (synopsis "HTS CRAM module for biogo") + (description "This package provides tools for handling CRAM files."))) + +(define-public go-github-com-biogo-hts-csi + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-csi") + (arguments + '(#:import-path "github.com/biogo/hts/csi" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (synopsis "Coordinate sorted indexing for biogo") + (description "This package implements CSIv1 and CSIv2 coordinate sorted +indexing."))) + +(define-public go-github-com-biogo-hts-fai + (package + (inherit go-github-com-biogo-hts-bam) + (name "go-github-com-biogo-hts-fai") + (arguments + '(#:import-path "github.com/biogo/hts/fai" + #:unpack-path "github.com/biogo/hts")) + (propagated-inputs + (list go-gopkg-in-check-v1)) + (synopsis "Fasta sequence file index handling for biogo") + (description "This package implements FAI fasta sequence file index +handling."))) + +(define-public go-github-com-biogo-biogo + (package + (name "go-github-com-biogo-biogo") + (version "1.0.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biogo/biogo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ali1mqf3dc26myv6l7wmqfr8i25461rbq3qdad8s0wi29622199")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/biogo/biogo")) + (propagated-inputs + (list go-gopkg-in-check-v1 + go-github-com-biogo-store-interval + go-github-com-biogo-store-kdtree + go-github-com-biogo-store-llrb + go-github-com-biogo-store-step + go-github-com-biogo-hts-bam + go-github-com-biogo-graph)) + (home-page "https://github.com/biogo/biogo") + (synopsis "Bioinformatics library for Go") + (description + "Bíogo is a bioinformatics library for the Go language.") + (license license:bsd-3))) |