diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 1897 |
1 files changed, 784 insertions, 1113 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8a00420946..13bd51860d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2017, 2021 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> @@ -161,6 +161,7 @@ #:use-module (gnu packages wget) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) + #:use-module (guix platform) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (ice-9 match)) @@ -210,85 +211,6 @@ tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.") (license license:gpl2))) -(define-public bamm - (package - (name "bamm") - (version "1.7.3") - (source (origin - (method git-fetch) - ;; BamM is not available on pypi. - (uri (git-reference - (url "https://github.com/Ecogenomics/BamM") - (commit version) - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) - (modules '((guix build utils))) - (snippet - `(begin - ;; Delete bundled htslib. - (delete-file-recursively "c/htslib-1.3.1"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; BamM is Python 2 only. - ;; Do not use bundled libhts. Do use the bundled libcfu because it has - ;; been modified from its original form. - #:configure-flags - ,#~(let ((htslib #$(this-package-input "htslib"))) - (list "--with-libhts-lib" (string-append htslib "/lib") - "--with-libhts-inc" (string-append htslib "/include/htslib"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ - (with-directory-excursion "c" - (let ((sh (which "sh"))) - (for-each make-file-writable (find-files "." ".*")) - ;; Use autogen so that 'configure' works. - (substitute* "autogen.sh" (("/bin/sh") sh)) - (setenv "CONFIG_SHELL" sh) - (invoke "./autogen.sh"))))) - (delete 'build) ;the build loops otherwise - (replace 'check - (lambda _ - ;; There are 2 errors printed, but they are safe to ignore: - ;; 1) [E::hts_open_format] fail to open file ... - ;; 2) samtools view: failed to open ... - (invoke "nosetests"))) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PATH")) - (pythonpath (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/bamm") - `("PATH" ":" prefix (,path)) - `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) - (native-inputs - (list autoconf - automake - libtool - zlib - python2-nose - python2-pysam)) - (inputs - (list htslib-1.3 ; At least one test fails on htslib-1.4+. - samtools - bwa - grep - sed - coreutils)) - (propagated-inputs - (list python2-numpy)) - (home-page "https://ecogenomics.github.io/BamM/") - (synopsis "Metagenomics-focused BAM file manipulator") - (description - "BamM is a C library, wrapped in python, to efficiently generate and -parse BAM files, specifically for the analysis of metagenomic data. For -instance, it implements several methods to assess contig-wise read coverage.") - (license license:lgpl3+))) - (define-public bamtools (package (name "bamtools") @@ -839,52 +761,6 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.") (license license:gpl3+))) -(define-public ribodiff - (package - (name "ribodiff") - (version "0.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ratschlab/RiboDiff") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz")))) - (build-system python-build-system) - (arguments - `(#: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")))))))) - (inputs - (list python2-numpy python2-matplotlib python2-scipy - python2-statsmodels)) - (native-inputs - (list python2-mock python2-nose)) - (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") - (synopsis "Detect translation efficiency changes from ribosome footprints") - (description "RiboDiff is a statistical tool that detects the protein -translational efficiency change from Ribo-Seq (ribosome footprinting) and -RNA-Seq data. It uses a generalized linear model to detect genes showing -difference in translational profile taking mRNA abundance into account. It -facilitates us to decipher the translational regulation that behave -independently with transcriptional regulation.") - (license license:gpl3+))) - (define-public bioawk (package (name "bioawk") @@ -1026,14 +902,6 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) -(define-public python2-pybedtools - (let ((pybedtools (package-with-python2 python-pybedtools))) - (package - (inherit pybedtools) - (native-inputs - (modify-inputs (package-native-inputs pybedtools) - (prepend python2-pathlib)))))) - (define-public python-biom-format (package (name "python-biom-format") @@ -1282,9 +1150,6 @@ into separate processes; and more.") (base32 "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))))) -(define-public python2-biopython - (package-with-python2 python-biopython)) - (define-public python-fastalite (package (name "python-fastalite") @@ -1305,9 +1170,6 @@ into separate processes; and more.") relying on a complex dependency tree.") (license license:expat))) -(define-public python2-fastalite - (package-with-python2 python-fastalite)) - (define-public biosoup (package (name "biosoup") @@ -2376,9 +2238,6 @@ SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It also includes an interface for tabix.") (license license:expat))) -(define-public python2-pysam - (package-with-python2 python-pysam)) - (define-public python-twobitreader (package (name "python-twobitreader") @@ -2439,59 +2298,60 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public tetoolkit (package (name "tetoolkit") - (version "2.0.3") + (version "2.2.1b") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mhammell-laboratory/tetoolkit") + (url "https://github.com/mhammell-laboratory/TEtranscripts") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807")))) + "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; not guaranteed to work with Python 3 - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'make-writable + (add-after 'unpack 'adjust-requirements (lambda _ - (for-each make-file-writable (find-files ".")) - #t)) + (substitute* "setup.py" + ;; This defunct dependency isn't required for Python 3 (see: + ;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111). + ((".*'argparse'.*") "")))) (add-after 'unpack 'patch-invocations (lambda* (#:key inputs #:allow-other-keys) (substitute* '("bin/TEtranscripts" "bin/TEcount") (("'sort ") - (string-append "'" (which "sort") " ")) + (string-append "'" (search-input-file inputs "bin/sort") " ")) (("'rm -f ") - (string-append "'" (which "rm") " -f ")) - (("'Rscript'") (string-append "'" (which "Rscript") "'"))) + (string-append "'" (search-input-file inputs "bin/rm") " -f ")) + (("'Rscript'") + (string-append "'" (search-input-file inputs "bin/Rscript") + "'"))) (substitute* "TEToolkit/IO/ReadInputs.py" - (("BamToBED") (which "bamToBed"))) + (("BamToBED") + (search-input-file inputs "bin/bamToBed"))) (substitute* "TEToolkit/Normalization.py" (("\"Rscript\"") - (string-append "\"" (which "Rscript") "\""))) - #t)) + (string-append "\"" (search-input-file inputs "bin/Rscript") + "\""))))) (add-after 'install 'wrap-program (lambda* (#:key outputs #:allow-other-keys) ;; Make sure the executables find R packages. - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (script) - (wrap-program (string-append out "/bin/" script) - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) - '("TEtranscripts" - "TEcount"))) - #t))))) + (for-each (lambda (script) + (wrap-program script + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + (list (search-input-file outputs "bin/TEtranscripts") + (search-input-file outputs "bin/TEcount")))))))) (inputs - (list coreutils + (list bash-minimal + coreutils bedtools - python2-argparse - python2-pysam + python-pysam r-minimal r-deseq2)) - (home-page "https://github.com/mhammell-laboratory/tetoolkit") + (home-page "https://github.com/mhammell-laboratory/TEtranscripts") (synopsis "Transposable elements in differential enrichment analysis") (description "This is package for including transposable elements in differential @@ -2902,9 +2762,6 @@ files.") accessing bigWig files.") (license license:expat))) -(define-public python2-pybigwig - (package-with-python2 python-pybigwig)) - (define-public python-schema-salad (package (name "python-schema-salad") @@ -3009,7 +2866,7 @@ and record oriented data modeling and the Semantic Web.") ;; Pytest doesn't know what to do with "-n auto" (substitute* "tox.ini" (("-n auto") ""))))))) - (propagated-inputs + (inputs (list python-argcomplete python-bagit python-coloredlogs @@ -3092,22 +2949,6 @@ writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.") (license license:bsd-3))) -(define-public python2-dendropy - (let ((base (package-with-python2 python-dendropy))) - (package/inherit base - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test - (lambda _ - ;; This test fails when the full test suite is run, as documented - ;; at https://github.com/jeetsukumaran/DendroPy/issues/74 - (substitute* "tests/test_dataio_nexml_reader_tree_list.py" - (("test_collection_comments_and_annotations") - "do_not_test_collection_comments_and_annotations")) - #t))) - ,@(package-arguments base)))))) - (define-public python-py2bit (package (name "python-py2bit") @@ -3304,6 +3145,11 @@ data and settings.") `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases + (add-before 'build 'set-force-source-date + ;; for reproducible dates, texlive needs this to respect respect + ;; SOURCE_DATE_EPOCH + (lambda _ + (setenv "FORCE_SOURCE_DATE" "1"))) (add-after 'unpack 'fix-latex-errors (lambda _ (with-fluids ((%default-port-encoding #f)) @@ -3816,96 +3662,6 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:bsd-3))) -(define-public fraggenescan - (package - (name "fraggenescan") - (version "1.30") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/fraggenescan/" - "FragGeneScan" version ".tar.gz")) - (sha256 - (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) - (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'patch-paths - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (share (string-append out "/share/fraggenescan/"))) - (substitute* "run_FragGeneScan.pl" - (("system\\(\"rm") - (string-append "system(\"" (which "rm"))) - (("system\\(\"mv") - (string-append "system(\"" (which "mv"))) - (("\\\"awk") (string-append "\"" (which "awk"))) - ;; This script and other programs expect the training files - ;; to be in the non-standard location bin/train/XXX. Change - ;; this to be share/fraggenescan/train/XXX instead. - (("^\\$train.file = \\$dir.*") - (string-append "$train_file = \"" - share - "train/\".$FGS_train_file;"))) - (substitute* "run_hmm.c" - (("^ strcat\\(train_dir, \\\"train/\\\"\\);") - (string-append " strcpy(train_dir, \"" share "/train/\");")))) - #t)) - (replace 'build - (lambda _ - (invoke "make" "clean") - (invoke "make" "fgs") - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (share (string-append out "/share/fraggenescan/train"))) - (install-file "run_FragGeneScan.pl" bin) - (install-file "FragGeneScan" bin) - (copy-recursively "train" share)) - #t)) - (delete 'check) - (add-after 'install 'post-install-check - ;; In lieu of 'make check', run one of the examples and check the - ;; output files gets created. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (frag (string-append bin "run_FragGeneScan.pl"))) - ;; Test complete genome. - (invoke frag - "-genome=./example/NC_000913.fna" - "-out=./test2" - "-complete=1" - "-train=complete") - (unless (and (file-exists? "test2.faa") - (file-exists? "test2.ffn") - (file-exists? "test2.gff") - (file-exists? "test2.out")) - (error "Expected files do not exist.")) - ;; Test incomplete sequences. - (invoke frag - "-genome=./example/NC_000913-fgs.ffn" - "-out=out" - "-complete=0" - "-train=454_30") - #t)))))) - (inputs - `(("perl" ,perl) - ("python" ,python-2))) ;not compatible with python 3. - (home-page "https://sourceforge.net/projects/fraggenescan/") - (synopsis "Finds potentially fragmented genes in short reads") - (description - "FragGeneScan is a program for predicting bacterial and archaeal genes in -short and error-prone DNA sequencing reads. It can also be applied to predict -genes in incomplete assemblies or complete genomes.") - ;; GPL3+ according to private correspondense with the authors. - (license license:gpl3+))) - (define-public fxtract (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) (package @@ -4027,48 +3783,6 @@ standard linear mixed model resolver with application in @acronym{GWAS, genome-wide association studies}.") (license license:gpl3))) -(define-public grit - (package - (name "grit") - (version "2.0.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/nboley/grit") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'generate-from-cython-sources - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete these C files to force fresh generation from pyx sources. - (delete-file "grit/sparsify_support_fns.c") - (delete-file "grit/call_peaks_support_fns.c") - (substitute* "setup.py" - (("Cython.Setup") "Cython.Build")) - #t))))) - (inputs - (list python2-scipy python2-numpy python2-pysam python2-networkx)) - (native-inputs - (list python2-cython)) - ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21. - (home-page "https://github.com/nboley/grit") - (synopsis "Tool for integrative analysis of RNA-seq type assays") - (description - "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify -full length transcript models. When none of these data sources are available, -GRIT can be run by providing a candidate set of TES or TSS sites. In -addition, GRIT can merge in reference junctions and gene boundaries. GRIT can -also be run in quantification mode, where it uses a provided GTF file and just -estimates transcript expression.") - (license license:gpl3+))) - (define-public hisat (package (name "hisat") @@ -4249,9 +3963,6 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) -(define-public python2-htseq - (package-with-python2 htseq)) - (define-public java-htsjdk (package (name "java-htsjdk") @@ -4788,7 +4499,7 @@ performance.") "--enable-libcurl" "--enable-s3"))) (inputs - (list curl openssl)) + (list bzip2 curl openssl xz)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs (list zlib)) @@ -4878,9 +4589,9 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (define htslib-for-stringtie (package - (inherit htslib) + (inherit htslib-1.12) (source (origin - (inherit (package-source htslib)) + (inherit (package-source htslib-1.12)) (patches (search-patches "htslib-for-stringtie.patch")))) (arguments @@ -5393,54 +5104,6 @@ unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.") (license license:gpl3+))) -(define-public miso - (let ((commit "b71402188000465e3430736a11ea118fd5639a4a") - (revision "1")) - (package - (name "miso") - (version (git-version "0.5.4" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/yarden/MISO/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5")) - (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - ;; Use "gcc" instead of "cc" for compilation. - (("^defines") - "cc.set_executables( -compiler='gcc', -compiler_so='gcc', -linker_exe='gcc', -linker_so='gcc -shared'); defines"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:tests? #f)) ; no "test" target - (inputs - ;; Samtools must not be newer than 1.2. See - ;; https://github.com/yarden/MISO/issues/135 - (list samtools-1.2 python2-numpy python2-pysam python2-scipy - python2-matplotlib)) - (native-inputs - (list python2-mock ; for tests - python2-pytz)) ; for tests - (home-page "https://miso.readthedocs.io/en/fastmiso/") - (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") - (description - "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates -the expression level of alternatively spliced genes from RNA-Seq data, and -identifies differentially regulated isoforms or exons across samples. By -modeling the generative process by which reads are produced from isoforms in -RNA-Seq, the MISO model uses Bayesian inference to compute the probability -that a read originated from a particular isoform.") - (license license:gpl2)))) - (define-public muscle (package (name "muscle") @@ -5531,80 +5194,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) -(define-public python2-pbcore - (package - (name "python2-pbcore") - (version "1.2.10") - (source (origin - (method url-fetch) - (uri (pypi-uri "pbcore" version)) - (sha256 - (base32 - "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ;pbcore < 2.0 requires Python 2.7 - #:phases (modify-phases %standard-phases - (add-after 'unpack 'remove-sphinx-dependency - (lambda _ - ;; Sphinx is only required for documentation tests, which - ;; we do not run; furthermore it depends on python2-sphinx - ;; which is no longer maintained. - (substitute* "requirements-dev.txt" - (("^sphinx") "")) - #t))))) - (propagated-inputs - (list python2-cython python2-numpy python2-pysam python2-h5py)) - (native-inputs - (list python2-nose python2-pyxb)) - (home-page "https://pacificbiosciences.github.io/pbcore/") - (synopsis "Library for reading and writing PacBio data files") - (description - "The pbcore package provides Python APIs for interacting with PacBio data -files and writing bioinformatics applications.") - (license license:bsd-3))) - -(define-public python2-warpedlmm - (package - (name "python2-warpedlmm") - (version "0.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "WarpedLMM" version ".zip")) - (sha256 - (base32 - "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; requires Python 2.7 - #:tests? #f ; test data are not included - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-weave - (lambda _ - (substitute* "warpedlmm/util/linalg.py" - (("from scipy import linalg, weave") - "from scipy import linalg\nimport weave")) - #t))))) - (propagated-inputs - (list python2-scipy - python2-numpy - python2-matplotlib - python2-fastlmm - python2-pandas - python2-pysnptools - python2-weave)) - (native-inputs - (list python2-mock python2-nose unzip)) - (home-page "https://github.com/PMBio/warpedLMM") - (synopsis "Implementation of warped linear mixed models") - (description - "WarpedLMM is a Python implementation of the warped linear mixed model, -which automatically learns an optimal warping function (or transformation) for -the phenotype as it models the data.") - (license license:asl2.0))) - (define-public prank (package (name "prank") @@ -5726,45 +5315,6 @@ clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.") (license license:gpl3+))) -(define-public pyicoteo - (package - (name "pyicoteo") - (version "2.0.7") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; does not work with Python 3 - #:tests? #f)) ; there are no tests - (inputs - (list python2-matplotlib)) - (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") - (synopsis "Analyze high-throughput genetic sequencing data") - (description - "Pyicoteo is a suite of tools for the analysis of high-throughput genetic -sequencing data. It works with genomic coordinates. There are currently six -different command-line tools: - -@enumerate -@item pyicoregion: for generating exploratory regions automatically; -@item pyicoenrich: for differential enrichment between two conditions; -@item pyicoclip: for calling CLIP-Seq peaks without a control; -@item pyicos: for genomic coordinates manipulation; -@item pyicoller: for peak calling on punctuated ChIP-Seq; -@item pyicount: to count how many reads from N experiment files overlap in a - region file; -@item pyicotrocol: to combine operations from pyicoteo. -@end enumerate\n") - (license license:gpl3+))) - (define-public prodigal (package (name "prodigal") @@ -6576,10 +6126,12 @@ simultaneously.") ;; architecture name ("i386") instead of the target system prefix ;; ("i686"). (mkdir (string-append (assoc-ref outputs "out") "/ilib")) - (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" - ,(system->linux-architecture - (or (%current-target-system) - (%current-system))) + (copy-recursively (string-append + "build/ncbi-vdb/linux/gcc/" + ,(platform-linux-architecture + (lookup-platform-by-target-or-system + (or (%current-target-system) + (%current-system)))) "/rel/ilib") (string-append (assoc-ref outputs "out") "/ilib")) @@ -6668,7 +6220,7 @@ subsequent visualization, annotation and storage of results.") (define-public plink-ng (package (inherit plink) (name "plink-ng") - (version "2.00a2.3") + (version "2.00a3-20220315") (source (origin (method git-fetch) @@ -6677,7 +6229,7 @@ subsequent visualization, annotation and storage of results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd")))) + (base32 "19inr47jwddkjb9kfb14yxc7xb16c73lkhgxj9sncb0fsiskb4x8")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -6832,9 +6384,6 @@ 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 python2-screed - (package-with-python2 python-screed)) - (define-public sra-tools (package (name "sra-tools") @@ -7821,7 +7370,7 @@ single-cell data.") r-rlist)) (home-page "https://github.com/soumelis-lab/ICELLNET") (synopsis "Transcriptomic-based framework to dissect cell communication") - (description "This packages provides a a transcriptomic-based framework + (description "This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based on transcriptomic profiles (gene @@ -8819,32 +8368,6 @@ regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.") (license license:gpl3+)))) -(define-public pepr - (package - (name "pepr") - (version "1.0.9") - (source (origin - (method url-fetch) - (uri (pypi-uri "PePr" version)) - (sha256 - (base32 - "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; python2 only - #:tests? #f)) ; no tests included - (propagated-inputs - (list python2-numpy python2-scipy python2-pysam)) - (home-page "https://github.com/shawnzhangyx/PePr") - (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") - (description - "PePr is a ChIP-Seq peak calling or differential binding analysis tool -that is primarily designed for data with biological replicates. It uses a -negative binomial distribution to model the read counts among the samples in -the same group, and look for consistent differences between ChIP and control -group or two ChIP groups run under different conditions.") - (license license:gpl3+))) - (define-public filevercmp (let ((commit "1a9b779b93d0b244040274794d402106907b71b7") (revision "1")) @@ -8981,6 +8504,34 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) +(define-public r-chromvarmotifs + (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") + (revision "1")) + (package + (name "r-chromvarmotifs") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/chromVARmotifs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) + (properties `((upstream-name . "chromVARmotifs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tfbstools" ,r-tfbstools))) + (home-page "https://github.com/GreenleafLab/chromVARmotifs") + (synopsis "Stores motif collections for use with motifmatchr or chromVAR") + (description + "This package stores motif collections as lists of @dfn{position +frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} +package for use in R with packages like @code{motifmatchr} or +@code{chromVAR}.") + (license license:expat)))) + (define-public r-raremetals2 (package (name "r-raremetals2") @@ -9009,6 +8560,43 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) +(define-public r-rnaseqdtu + (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac") + (revision "1")) + (package + (name "r-rnaseqdtu") + (version (git-version "2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mikelove/rnaseqDTU/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0")))) + (properties `((upstream-name . "rnaseqDTU"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-devtools + r-dexseq + r-drimseq + r-edger + r-rafalib + r-stager)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/rnaseqDTU/") + (synopsis "RNA-seq workflow for differential transcript usage") + (description + "This package provides an RNA-seq workflow for differential transcript +usage (DTU) following Salmon quantification. This workflow performs a DTU +analysis on simulated data. It also shows how to use stageR to perform +two-stage testing of DTU, a statistical framework to screen at the gene level +and then confirm which transcripts within the significant genes show evidence +of DTU.") + (license license:artistic2.0)))) + (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -9101,6 +8689,44 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba") @@ -9267,72 +8893,6 @@ adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.") (license license:gpl3+))) -(define-public gess - (package - (name "gess") - (version "1.0") - (source (origin - (method url-fetch) - (uri (string-append "http://compbio.uthscsa.edu/" - "GESS_Web/files/" - "gess-" version ".src.tar.gz")) - (sha256 - (base32 - "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((python (assoc-ref inputs "python")) - (out (assoc-ref outputs "out")) - (bin (string-append out "/bin/")) - (target (string-append - out "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages/gess/"))) - (mkdir-p target) - (copy-recursively "." target) - ;; Make GESS.py executable - (chmod (string-append target "GESS.py") #o555) - ;; Add Python shebang to the top and make Matplotlib - ;; usable. - (substitute* (string-append target "GESS.py") - (("\"\"\"Description:" line) - (string-append "#!" (which "python") " -import matplotlib -matplotlib.use('Agg') -" line))) - ;; Make sure GESS has all modules in its path - (wrap-script (string-append target "GESS.py") - #:guile (search-input-file inputs "bin/guile") - `("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_PYTHONPATH")))) - (mkdir-p bin) - (symlink (string-append target "GESS.py") - (string-append bin "GESS.py")) - #t)))))) - (inputs - `(("python" ,python-2) - ("python2-pysam" ,python2-pysam) - ("python2-scipy" ,python2-scipy) - ("python2-numpy" ,python2-numpy) - ("python2-networkx" ,python2-networkx) - ("python2-biopython" ,python2-biopython) - ("guile" ,guile-3.0))) ; for the script wrapper - (home-page "https://compbio.uthscsa.edu/GESS_Web/") - (synopsis "Detect exon-skipping events from raw RNA-seq data") - (description - "GESS is an implementation of a novel computational method to detect de -novo exon-skipping events directly from raw RNA-seq data without the prior -knowledge of gene annotation information. GESS stands for the graph-based -exon-skipping scanner detection scheme.") - (license license:bsd-3))) - (define-public phylip (package (name "phylip") @@ -10266,7 +9826,7 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.17") + (version "3.0.7") ;; The tarball on Pypi does not include the tests. (source (origin (method git-fetch) @@ -10276,16 +9836,33 @@ variational inference.") (file-name (git-file-name name version)) (sha256 (base32 - "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) + "0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check + ;; See https://github.com/linnarsson-lab/loompy/issues/169 + (add-after 'unpack 'fix-h5py-error + (lambda _ + (substitute* "tests/test_file_attribute_manager.py" + (("h5py.File\\(f.name\\)") + "h5py.File(f.name, 'a')")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir (lambda _ - (invoke "pytest" "tests")))))) + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "tests"))))))) (propagated-inputs - (list python-h5py python-numpy python-pandas python-scipy)) + (list python-click + python-h5py + python-numba + python-numpy + python-numpy-groupies + python-pandas + python-scipy)) (native-inputs (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") @@ -10869,7 +10446,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.19") + (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10877,8 +10454,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm")) - (patches (search-patches "pigx-rnaseq-no-citeproc.patch")))) + "0acdjimfb9ywba8zsv7lavv436pmcmp8ra683h11wr4s3681pqk8")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10909,6 +10485,7 @@ once. This package provides tools to perform Drop-seq analyses.") sed gzip snakemake + megadepth multiqc star-for-pigx hisat2 @@ -10954,7 +10531,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.53") + (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -10962,16 +10539,12 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h")) - (patches (search-patches "pigx-chipseq-no-citeproc.patch")))) + "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) @@ -11025,7 +10598,7 @@ expression report comparing samples in an easily configurable manner.") bedtools kentutils)) (native-inputs - (list autoconf automake python-pytest)) + (list python-pytest)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak @@ -11040,7 +10613,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -11048,8 +10621,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1dipikph0xdr8fp0h1flpafcrg60y4aabljg8fl1v92j3gxdggmw")) - (patches (search-patches "pigx-bsseq-no-citeproc.patch")))) + "1hfiignq3410dbl6f67vc6zr69abknpcgxixx475dspky2jb5lyn")))) (build-system gnu-build-system) (arguments `(;; TODO: tests currently require 12+GB of RAM. See @@ -11057,9 +10629,6 @@ in an easily configurable manner.") #:tests? #f #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) @@ -11071,7 +10640,7 @@ in an easily configurable manner.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list tzdata automake autoconf)) + (list tzdata)) (inputs (list coreutils sed @@ -11115,7 +10684,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.7") + (version "1.1.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -11123,65 +10692,63 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")) - (patches (search-patches "pigx-scrnaseq-no-citeproc.patch")))) + "0adx7877c3lhlrzfid76i8bc829wcmzvrm0jx47gyid8mxqb7vqs")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) - (add-before 'configure 'set-PYTHONPATH + (add-before 'configure 'set-additional-environment-variables (lambda _ + ;; Needed because of loompy + (setenv "NUMBA_CACHE_DIR" "/tmp") + ;; Needed to capture environment (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) - (native-inputs - (list automake autoconf)) (inputs - `(("coreutils" ,coreutils) - ("perl" ,perl) - ("fastqc" ,fastqc) - ("flexbar" ,flexbar) - ("java" ,icedtea-8) - ("jellyfish" ,jellyfish) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-pandas" ,python-pandas) - ("python-magic" ,python-magic) - ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy) - ("pandoc" ,pandoc) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("star" ,star-for-pigx) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-dropbead" ,r-dropbead) - ("r-dt" ,r-dt) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hdf5array" ,r-hdf5array) - ("r-pheatmap" ,r-pheatmap) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rtsne" ,r-rtsne) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-seurat" ,r-seurat) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-yaml" ,r-yaml))) + (list coreutils + perl + fastqc + flexbar + icedtea-8 + jellyfish + python-wrapper + python-pyyaml + python-pandas + python-magic + python-numpy + python-loompy + pandoc + samtools + snakemake + star-for-pigx + r-minimal + r-argparser + r-cowplot + r-data-table + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-dropbead + r-dt + r-genomicalignments + r-genomicfiles + r-genomicranges + r-ggplot2 + r-hdf5array + r-pheatmap + r-rmarkdown + r-rsamtools + r-rtracklayer + r-rtsne + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-stringr + r-yaml)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") - (description "PiGX scRNAseq is an analysis pipeline for preprocessing and + (description + "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are read files from the sequencing experiment, and a configuration file which describes the experiment. It produces processed files for downstream analysis @@ -11189,25 +10756,29 @@ and interactive quality reports. The pipeline is designed to work with UMI based methods.") (license license:gpl3+))) -(define-public pigx-sars-cov2-ww +(define-public pigx-sars-cov-2 (package - (name "pigx-sars-cov2-ww") - (version "0.0.4") + (name "pigx-sars-cov-2") + (version "0.0.7") (source (origin (method url-fetch) - (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" - "releases/download/v" version - "/pigx_sars-cov2-ww-" version ".tar.gz")) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sars-cov-2" + "/releases/download/v" version + "/pigx_sars-cov-2-" version ".tar.gz")) (sha256 (base32 - "0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs")) - (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch")))) + "1bqm03ypf7l8lrkjkydxzn7vy0qlps3v9c5cpz2wb008zw44bi3k")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:tests? #f ;requires huge kraken database + #:phases (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ + ;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123 + (substitute* "m4/ax_r_package.m4" + (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") + "if(system.file(package=\"PKG\") == \"\")")) (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ @@ -11216,7 +10787,6 @@ based methods.") (list automake autoconf)) (inputs (list bash-minimal - bbmap bedtools bwa ensembl-vep @@ -11227,7 +10797,6 @@ based methods.") krona-tools lofreq multiqc - prinseq python-pyyaml python-wrapper r-base64url @@ -11243,6 +10812,7 @@ based methods.") r-rmarkdown r-stringr r-tidyr + r-viridis samtools snakemake wget)) @@ -11255,6 +10825,9 @@ 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-public pigx (package (name "pigx") @@ -11813,6 +11386,105 @@ distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.") (license license:cc0)))) +;; There have been no releases. +(define-public r-cytobackbone + (let ((commit "4c1a0a35cc5ae1f8f516127cec92351d96fe26e7") + (revision "1")) + (package + (name "r-cytobackbone") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchitchek-lab/CytoBackBone") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahiad14zcgdk42xzw5xryic2ibn2l8lkrcdvl2b5sz2js028yb3")))) + (properties `((upstream-name . "CytoBackBone"))) + (build-system r-build-system) + (propagated-inputs + (list r-flowcore + r-flowutils + r-fnn + r-ggplot2 + r-preprocesscore)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tchitchek-lab/CytoBackBone") + (synopsis "Merge phenotype information from different cytometric profiles") + (description + "This package implements an algorithm which increases the number of +simultaneously measurable markers and in this way helps with study of the +immune responses. Thus, the present algorithm, named @code{CytoBackBone}, +allows combining phenotypic information of cells from different cytometric +profiles obtained from different cytometry panels. This computational +approach is based on the principle that each cell has its own phenotypic and +functional characteristics that can be used as an identification card. +@code{CytoBackBone} uses a set of predefined markers, that we call the +backbone, to define this identification card. The phenotypic information of +cells with similar identification cards in the different cytometric profiles +is then merged.") + (license license:gpl2)))) + +(define-public r-giotto + (let ((commit "68d7390dce87223cac11d4d8f31705fe0144d011") + (revision "1")) + (package + (name "r-giotto") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/RubD/Giotto/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mv60khc05wrxzr4ir6cirn7dpqvgwan5hm00lmafsyalr51nf5i")))) + (properties `((upstream-name . "Giotto"))) + (build-system r-build-system) + (propagated-inputs + (list r-clusterr + r-complexheatmap + r-cowplot + r-data-table + r-dbscan + r-deldir + r-farver + r-fitdistrplus + r-ggdendro + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-irlba + r-lfa + r-limma + r-magick + r-magrittr + r-matrix + r-matrixstats + r-plotly + r-qvalue + r-r-utils + r-rcolorbrewer + r-rcpp + r-reshape2 + r-reticulate + r-rfast + r-rlang + r-rtsne + r-scales + r-uwot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RubD/Giotto/") + (synopsis "Spatial single-cell transcriptomics toolbox") + (description + "This package provides a toolbox to process, analyze and visualize +spatial single-cell expression data.") + (license license:expat)))) + (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 @@ -11874,56 +11546,6 @@ conversions, region filtering, FASTA sequence extraction and more.") (license (list license:expat license:artistic2.0))))) -(define-public find-circ - ;; The last release was in 2015. The license was clarified in 2017, so we - ;; take the latest commit. - (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d") - (revision "1")) - (package - (name "find-circ") - (version (git-version "1.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/marvin-jens/find_circ") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; there are none - #:phases - ;; There is no actual build system. - (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")) - (path (getenv "GUIX_PYTHONPATH"))) - (for-each (lambda (script) - (install-file script bin) - (wrap-program (string-append bin "/" script) - `("GUIX_PYTHONPATH" ":" prefix (,path)))) - '("cmp_bed.py" - "find_circ.py" - "maxlength.py" - "merge_bed.py" - "unmapped2anchors.py"))) - #t))))) - (inputs - (list python-2 python2-pysam python2-numpy)) - (home-page "https://github.com/marvin-jens/find_circ") - (synopsis "circRNA detection from RNA-seq reads") - (description "This package provides tools to detect head-to-tail -spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) -in RNA-seq data.") - (license license:gpl3)))) - (define-public fit-sne (package (name "fit-sne") @@ -11990,7 +11612,7 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.8.2") + (version "1.9.1") (source (origin (method git-fetch) @@ -12000,7 +11622,7 @@ implementation differs in these ways: (file-name (git-file-name name version)) (sha256 (base32 - "14zax23lqinv7xyv3491vpl3ydi38naiwaxg5mkfs5zk2406cqdr")))) + "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) (build-system python-build-system) (arguments `(#:phases @@ -12020,6 +11642,10 @@ implementation differs in these ways: (invoke "python" "-m" "pip" "install" wheel (string-append "--prefix=" out))) (find-files "dist" "\\.whl$"))))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) (replace 'check (lambda* (#:key tests? inputs #:allow-other-keys) (when tests? @@ -12027,6 +11653,7 @@ implementation differs in these ways: (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_normalization.py") (delete-file "scanpy/tests/test_score_genes.py") (delete-file "scanpy/tests/test_highly_variable_genes.py") @@ -12035,6 +11662,9 @@ implementation differs in these ways: (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; These two fail with "ValueError: I/O operation on closed file." + (delete-file "scanpy/tests/test_neighbors_key_added.py") + ;; TODO: these fail with TypingError and "Use of unsupported ;; NumPy function 'numpy.split'". (delete-file "scanpy/tests/test_metrics.py") @@ -12060,17 +11690,20 @@ implementation differs in these ways: " and not test_clustermap" ;; These try to connect to the network + " and not test_scrublet_plots" " and not test_plot_rank_genes_groups_gene_symbols" + " and not test_pca_n_pcs" " and not test_pca_chunked" " and not test_pca_sparse" " and not test_pca_reproducible")))))))) (propagated-inputs (list python-anndata + python-dask python-h5py python-igraph python-joblib python-legacy-api-wrap - python-louvain-0.7 + python-louvain python-matplotlib python-natsort python-networkx @@ -12081,6 +11714,7 @@ implementation differs in these ways: python-scikit-learn python-scipy python-seaborn + python-session-info python-sinfo python-statsmodels python-tables @@ -12417,9 +12051,6 @@ bgzipped text file that contains a pair of genomic coordinates per line.") fasta subsequences.") (license license:bsd-3))) -(define-public python2-pyfaidx - (package-with-python2 python-pyfaidx)) - (define-public python-cooler (package (name "python-cooler") @@ -12435,6 +12066,13 @@ fasta subsequences.") (arguments `(#:phases (modify-phases %standard-phases + ;; cooler requests cytoolz<0.11. It only uses cytoolz for "compose", + ;; which composes two functions. + (add-after 'unpack 'use-recent-cytoolz + (lambda _ + (substitute* '("requirements.txt" + "cooler.egg-info/requires.txt") + (("cytoolz.*<.*0.11") "cytoolz")))) (add-after 'unpack 'patch-tests (lambda _ (substitute* "tests/test_create.py" @@ -12460,7 +12098,7 @@ fasta subsequences.") (list python-asciitree python-biopython python-click - python-cytoolz-for-cooler + python-cytoolz python-dask python-h5py python-multiprocess @@ -12667,7 +12305,20 @@ efficiently.") (lambda _ (for-each make-file-writable (list "test_data/hic2cool_0.4.2_single_res.cool" - "test_data/hic2cool_0.7.0_multi_res.mcool"))))))) + "test_data/hic2cool_0.7.0_multi_res.mcool")))) + ;; See https://github.com/4dn-dcic/hic2cool/issues/58 + (add-after 'unpack 'fix-incompatibility-with-h5py-3 + (lambda _ + (substitute* "test.py" + (("h5py.File\\(fname\\)") "h5py.File(fname, 'r')")) + (substitute* "hic2cool/hic2cool_updates.py" + (("h5py.File\\(writefile\\)") + "h5py.File(writefile, 'a')")))) + ;; These two tests fail for unknown reasons. + (add-after 'unpack 'disable-broken-tests + (lambda _ + (substitute* "test.py" + (("def test_convert") "def _test_convert"))))))) (propagated-inputs (list python-cooler python-h5py python-numpy python-pandas python-scipy)) @@ -12844,42 +12495,6 @@ of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.") (license license:gpl3+)))) -(define-public poretools - ;; The latest release was in 2016 and the latest commit is from 2017 - ;; the recommended way to install is to clone the git repository - ;; https://poretools.readthedocs.io/en/latest/content/installation.html - (let ((commit "e426b1f09e86ac259a00c261c79df91510777407") - (revision "1")) - (package - (name "poretools") - (version (git-version "0.6.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/arq5x/poretools") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am")))) - (build-system python-build-system) - ;; requires python >=2.7, <3.0, and the same for python dependencies - (arguments `(#:python ,python-2)) - (inputs - (list hdf5)) - (propagated-inputs - (list python2-dateutil python2-h5py python2-matplotlib - python2-pandas python2-seaborn)) - (home-page "https://poretools.readthedocs.io") - (synopsis "Toolkit for working with nanopore sequencing data") - (description - "The MinION from Oxford Nanopore Technologies is a nanopore sequencer. -This @code{poretools} package is a flexible toolkit for exploring datasets -generated by nanopore sequencing devices for the purposes of quality control and -downstream analysis. Poretools operates directly on the native FAST5, a variant -of the Hierarchical Data Format (HDF5) standard.") - (license license:expat)))) - (define-public jamm (package (name "jamm") @@ -13461,6 +13076,13 @@ repeated areas between contigs.") (snippet '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-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)) (propagated-inputs @@ -13585,162 +13207,6 @@ Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.") (license license:gpl3+))) -(define-public pplacer - (let ((commit "807f6f3")) - (package - (name "pplacer") - ;; The commit should be updated with each version change. - (version "1.1.alpha19") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/matsen/pplacer") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) - (build-system ocaml-build-system) - (arguments - `(#:modules ((guix build ocaml-build-system) - (guix build utils) - (ice-9 ftw)) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-build-with-latest-ocaml - (lambda _ - (substitute* "myocamlbuild.ml" - (("dep \\[\"c_pam\"\\]" m) - (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n" - m)) - (("let run_and_read" m) - (string-append " -let split s ch = - let x = ref [] in - let rec go s = - let pos = String.index s ch in - x := (String.before s pos)::!x; - go (String.after s (pos + 1)) - in - try go s - with Not_found -> !x -let split_nl s = split s '\\n' -let before_space s = - try String.before s (String.index s ' ') - with Not_found -> s - -" m)) - (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) - (string-append "List.map before_space (split_nl & " m ")")) - ((" blank_sep_strings &") "") - ((" Lexing.from_string &") "")) - #t)) - (add-after 'unpack 'replace-bundled-cddlib - (lambda* (#:key inputs #:allow-other-keys) - (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) - (local-dir "cddlib_guix")) - (mkdir local-dir) - (with-directory-excursion local-dir - (invoke "tar" "xvf" cddlib-src)) - (let ((cddlib-src-folder - (string-append local-dir "/" - (list-ref (scandir local-dir) 2) - "/lib-src"))) - (for-each make-file-writable (find-files "cdd_src" ".*")) - (for-each - (lambda (file) - (copy-file file - (string-append "cdd_src/" (basename file)))) - (find-files cddlib-src-folder ".*[ch]$"))) - #t))) - (add-after 'unpack 'fix-makefile - (lambda _ - ;; Remove system calls to 'git'. - (substitute* "Makefile" - (("^DESCRIPT:=pplacer-.*") - (string-append - "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) - (substitute* "myocamlbuild.ml" - (("git describe --tags --long .*\\\" with") - (string-append - "echo -n v" ,version "-" ,commit "\" with"))) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (copy-recursively "bin" bin)) - #t))) - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib)) - (inputs - `(("zlib" ,zlib "static") - ("gsl" ,gsl-static) - ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit)) - ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries)) - ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip)) - ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv)) - ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3)) - ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm)) - ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl)) - ("ocaml-gsl" ,ocaml4.07-gsl-1) - ("sqlite:static" ,sqlite "static"))) - (native-inputs - `(("cddlib-src" ,(package-source cddlib)) - ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) - ("pkg-config" ,pkg-config))) - (propagated-inputs - (list pplacer-scripts)) - (synopsis "Phylogenetic placement of biological sequences") - (description - "Pplacer places query sequences on a fixed reference phylogenetic tree -to maximize phylogenetic likelihood or posterior probability according to a -reference alignment. Pplacer is designed to be fast, to give useful -information about uncertainty, and to offer advanced visualization and -downstream analysis.") - (home-page "https://matsen.fhcrc.org/pplacer/") - (license license:gpl3)))) - -;; This package is installed alongside 'pplacer'. It is a separate package so -;; that it can use the python-build-system for the scripts that are -;; distributed alongside the main OCaml binaries. -(define pplacer-scripts - (package - (inherit pplacer) - (name "pplacer-scripts") - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts") #t)) - (replace 'check - (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) - (add-after 'install 'wrap-executables - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin:" - (assoc-ref inputs "infernal") "/bin"))) - (display path) - (wrap-program (string-append bin "/refpkg_align.py") - `("PATH" ":" prefix (,path)))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin"))) - (wrap-program (string-append bin "/hrefpkg_query.py") - `("PATH" ":" prefix (,path))))) - #t))))) - (inputs - `(("infernal" ,infernal) - ("hmmer" ,hmmer))) - (propagated-inputs - `(("python-biopython" ,python2-biopython) - ("taxtastic" ,taxtastic))) - (synopsis "Pplacer Python scripts"))) - (define-public checkm (package (name "checkm") @@ -13778,9 +13244,6 @@ on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.") (license license:gpl3+))) -(define-public python2-checkm-genome - (deprecated-package "python2-checkm-genome" checkm)) - (define-public umi-tools (package (name "umi-tools") @@ -14040,49 +13503,51 @@ mutations from scRNA-Seq data.") (name "tabixpp") (version "1.1.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) - (modules '((guix build utils))) - (snippet - `(begin - (delete-file-recursively "htslib") #t)))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "htslib"))))) (build-system gnu-build-system) (inputs - (list htslib zlib)) + (list bzip2 htslib xz zlib)) (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - ;; The build phase needs overriding the location of htslib. - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "INCLUDES= -I" htslib-ref "/include/htslib") - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include")) - (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (install-file "tabix++" bin) - (install-file "libtabixpp.so" lib) - (install-file "libtabixpp.a" lib) - (install-file "tabix.hpp" (string-append out "/include")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") - (lambda _ - (format #t "prefix=~a~@ + (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "CXX=" #$(cxx-for-target)) + "HTS_HEADERS=" + (string-append "HTS_LIB=" + (search-input-file %build-inputs + "/lib/libhts.a")) + "INCLUDES=") + #:tests? #f ; There are no tests to run. + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; Build shared and static libraries. + (add-after 'build 'build-libraries + (lambda* (#:key inputs #:allow-other-keys) + (invoke #$(cxx-for-target) + "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke #$(ar-for-target) "rcs" "libtabixpp.a" "tabix.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "tabix++" bin) + (install-file "libtabixpp.so" lib) + (install-file "libtabixpp.a" lib) + (install-file "tabix.hpp" (string-append out "/include")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14093,8 +13558,7 @@ mutations from scRNA-Seq data.") Description: C++ wrapper around tabix project~@ Libs: -L${libdir} -ltabixpp~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts @@ -14116,57 +13580,106 @@ some of the details of opening and jumping in tabix-indexed files.") (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests to run. - #:make-flags '("libsw.a" "all") + (list + #:tests? #f ; There are no tests to run. + #:make-flags + #~(list (string-append "CXX=" #$(cxx-for-target)) + "libsw.a" "all") #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "Makefile" - (("-c ") "-c -fPIC ")) - #t)) - (add-after 'build 'build-dynamic - (lambda _ - (invoke "g++" - "-shared" "-o" "libsmithwaterman.so" - "smithwaterman.o" "SmithWatermanGotoh.o" - "disorder.o" "BandedSmithWaterman.o" - "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib"))) - (install-file "smithwaterman" bin) - (for-each - (lambda (file) - (install-file file (string-append out "/include/smithwaterman"))) - (find-files "." "\\.h$")) - (install-file "libsmithwaterman.so" lib) - (install-file "libsw.a" lib) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") - (lambda _ - (format #t "prefix=~a~@ - exec_prefix=${prefix}~@ - libdir=${exec_prefix}/lib~@ - includedir=${prefix}/include/smithwaterman~@ - ~@ - ~@ - Name: smithwaterman~@ - Version: ~a~@ - Description: smith-waterman-gotoh alignment algorithm~@ - Libs: -L${libdir} -lsmithwaterman~@ - Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #$@(if (%current-target-system) + #~((substitute* "Makefile" + (("\tld") + (string-append "\t" #$(%current-target-system) "-ld")) + (("\tar") + (string-append "\t" #$(%current-target-system) "-ar")))) + '()))) + (add-after 'build 'build-dynamic + (lambda _ + (invoke #$(cxx-for-target) + "-shared" "-o" "libsmithwaterman.so" + "smithwaterman.o" "SmithWatermanGotoh.o" + "disorder.o" "BandedSmithWaterman.o" + "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) + (install-file "smithwaterman" bin) + (for-each + (lambda (file) + (install-file file (string-append out "/include/smithwaterman"))) + (find-files "." "\\.h$")) + (install-file "libsmithwaterman.so" lib) + (install-file "libsw.a" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/smithwaterman~@ + ~@ + ~@ + Name: smithwaterman~@ + Version: ~a~@ + Description: smith-waterman-gotoh alignment algorithm~@ + Libs: -L${libdir} -lsmithwaterman~@ + Cflags: -I${includedir}~%" + out #$version))))))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") (description "Implementation of the Smith-Waterman algorithm.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) +(define-public sylamer + (package + (name "sylamer") + (version "18-131") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/micans/sylamer/") + (commit "aa75c3584797c0c15f860addb645f7bc1dd7627d"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ddiwlrdghhb4574rvfw0brjp9gs5l6nfsy82h0m4mvz1dr3gkj5")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no test target + #:make-flags + #~(list (string-append "GSLPREFIX=" #$(this-package-input "gsl"))) + #:phases + '(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("cp sylamer \\$\\(HOME\\)/local/bin") + (string-append "install -D -t " (assoc-ref outputs "out") + "/bin sylamer"))) + (install-file "Makefile" "src") + (chdir "src")))))) + (inputs (list gsl zlib)) + (home-page "https://www.ebi.ac.uk/research/enright/software/sylamer") + (synopsis "Asses microRNA binding and siRNA off-target effects") + (description "Sylamer is a system for finding significantly over or +under-represented words in sequences according to a sorted gene list. +Typically it is used to find significant enrichment or depletion of microRNA +or siRNA seed sequences from microarray expression data. Sylamer is extremely +fast and can be applied to genome-wide datasets with ease. Results are +plotted in terms of a significance landscape plot. These plots show +significance profiles for each word studied across the sorted genelist.") + (license license:gpl3+))) + (define-public multichoose (package (name "multichoose") @@ -14250,36 +13763,37 @@ neural networks.") (base32 "0rp1blskhzxf7vbh253ibpxbgl9wwgyzf1wbkxndi08d3j4vcss9")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "Makefile" - (("-c ") "-c -fPIC ")) - #t)) - (add-after 'build 'build-dynamic - (lambda _ - (invoke "g++" - "-shared" "-o" "libfastahack.so" - "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (mkdir-p (string-append out "/include/fastahack")) - (for-each - (lambda (file) - (install-file file (string-append out "/include/fastahack"))) - (find-files "." "\\.h$")) - (install-file "fastahack" bin) - (install-file "libfastahack.so" lib) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (list #:make-flags #~(list (string-append "CXX=" #$(cxx-for-target))) + ;; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")))) + (add-after 'build 'build-dynamic (lambda _ - (format #t "prefix=~a~@ + (invoke #$(cxx-for-target) + "-shared" "-o" "libfastahack.so" + "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (mkdir-p (string-append out "/include/fastahack")) + (for-each + (lambda (file) + (install-file file (string-append out "/include/fastahack"))) + (find-files "." "\\.h$")) + (install-file "fastahack" bin) + (install-file "libfastahack.so" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include/fastahack~@ @@ -14290,8 +13804,7 @@ neural networks.") Description: Indexing and sequence extraction from FASTA files~@ Libs: -L${libdir} -lfastahack~@ Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + out #$version))))))))) (home-page "https://github.com/ekg/fastahack") (synopsis "Indexing and sequence extraction from FASTA files") (description "Fastahack is a small application for indexing and @@ -14304,7 +13817,7 @@ library automatically handles index file generation and use.") (define-public vcflib (package (name "vcflib") - (version "1.0.2") + (version "1.0.3") (source (origin (method git-fetch) @@ -14313,31 +13826,30 @@ library automatically handles index file generation and use.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh")) + (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) (modules '((guix build utils))) (snippet - '(begin - (substitute* "CMakeLists.txt" - ((".*fastahack.*") "") - ((".*smithwaterman.*") "") - (("(pkg_check_modules\\(TABIXPP)" text) - (string-append + #~(begin + (substitute* "CMakeLists.txt" + ((".*fastahack.*") "") + ((".*smithwaterman.*") "") + (("(pkg_check_modules\\(TABIXPP)" text) + (string-append "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) - (("\\$\\{TABIXPP_LIBRARIES\\}" text) - (string-append "${FASTAHACK_LIBRARIES} " - "${SMITHWATERMAN_LIBRARIES} " - text))) - (substitute* (find-files "." "\\.(h|c)(pp)?$") - (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") - (("\"convert.h\"") "<smithwaterman/convert.h>") - (("\"disorder.h\"") "<smithwaterman/disorder.h>") - (("Fasta.h") "fastahack/Fasta.h")) - (for-each delete-file-recursively - '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")) - #t)))) + (("\\$\\{TABIXPP_LIBRARIES\\}" text) + (string-append "${FASTAHACK_LIBRARIES} " + "${SMITHWATERMAN_LIBRARIES} " + text))) + (substitute* (find-files "." "\\.(h|c)(pp)?$") + (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") + (("\"convert.h\"") "<smithwaterman/convert.h>") + (("\"disorder.h\"") "<smithwaterman/disorder.h>") + (("Fasta.h") "fastahack/Fasta.h")) + (for-each delete-file-recursively + '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" + "libVCFH" "multichoose" "smithwaterman")))))) (build-system cmake-build-system) (inputs (list bzip2 @@ -14358,41 +13870,47 @@ library automatically handles index file generation and use.") ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-shared-library - (lambda _ - (substitute* "CMakeLists.txt" - (("vcflib STATIC") "vcflib SHARED")) - (substitute* "test/Makefile" - (("libvcflib.a") "libvcflib.so")) - #t)) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (mkdir target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose")) - #t))) - ;; This pkg-config file is provided by other distributions. - (add-after 'install 'install-pkg-config-file - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pkgconfig (string-append out "/lib/pkgconfig"))) - (mkdir-p pkgconfig) - (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (list #:configure-flags + #~(list (string-append + "-DPKG_CONFIG_EXECUTABLE=" + (search-input-file + %build-inputs (string-append + "/bin/" #$(pkg-config-for-target))))) + #:tests? #f ; no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-shared-library (lambda _ - (format #t "prefix=~a~@ + (substitute* "CMakeLists.txt" + (("vcflib STATIC") "vcflib SHARED")) + (substitute* "test/Makefile" + (("libvcflib.a") "libvcflib.so")))) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (mkdir target) + (with-directory-excursion target + (let ((source (or (assoc-ref inputs source) + (assoc-ref native-inputs source)))) + (if (file-is-directory? source) + (copy-recursively source ".") + (invoke "tar" "xvf" + source + "--strip-components=1"))))))) + (and + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "intervaltree-src" "intervaltree") + (unpack "multichoose-src" "multichoose"))))) + ;; This pkg-config file is provided by other distributions. + (add-after 'install 'install-pkg-config-file + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pkgconfig (string-append out "/lib/pkgconfig"))) + (mkdir-p pkgconfig) + (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14403,8 +13921,7 @@ library automatically handles index file generation and use.") Description: C++ library for parsing and manipulating VCF files~@ Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret @@ -14441,6 +13958,7 @@ manipulations on VCF files.") ("parallel" ,parallel) ("perl" ,perl) ("pkg-config" ,pkg-config) + ("python" ,python) ("samtools" ,samtools) ("simde" ,simde) ;; This submodule is needed to run the tests. @@ -15275,11 +14793,11 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c") - (revision "1")) + (let ((commit "458e647b503c3472b0b98c0aeca934f452e039ee") + (revision "2")) (package (name "r-signac") - (version (git-version "1.1.1" revision commit)) + (version (git-version "1.6.0" revision commit)) (source (origin (method git-fetch) @@ -15288,16 +14806,12 @@ translates between different variant encodings.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 - "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) + (base32 "1hgwpgighkvfkai80n4d2252s4sdpa4faag4ncdiylicl5wa7lbj")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs - (list r-annotationfilter - r-biocgenerics - r-biostrings - r-biovizbase + (list r-biocgenerics r-data-table r-dplyr r-fastmatch @@ -15305,7 +14819,6 @@ translates between different variant encodings.") r-future-apply r-genomeinfodb r-genomicranges - r-ggbio r-ggforce r-ggplot2 r-ggrepel @@ -15316,6 +14829,7 @@ translates between different variant encodings.") r-matrix r-patchwork r-pbapply + r-qlcmatrix r-rcpp r-rcpproll r-rsamtools @@ -15324,7 +14838,8 @@ translates between different variant encodings.") r-seurat r-seuratobject r-stringi - r-tidyr)) + r-tidyr + r-tidyselect)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description @@ -15722,7 +15237,11 @@ populations.") (file-name (git-file-name name version)) (sha256 (base32 - "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")))) + "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")) + (snippet + #~(begin + (use-modules ((guix build utils))) + (delete-file "src/scregseg/_utils.c"))))) (build-system python-build-system) (arguments `(#:tests? #false ; tests require network access @@ -16069,3 +15588,155 @@ workflows from concise descriptions in ccwl. It is implemented as an @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "<atomic_queue/atomic_queue.h>")) + ;; Remove compiler optimizations. + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16 ") "") + (("-march=native ") "")) + ;; Allow building on architectures other than x86_64. + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0")))))) + (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + ;; Adapted from .github/workflows/test_on_push.yml + (lambda* (#:key tests? inputs #:allow-other-keys) + (when tests? + (let ((samtools (search-input-file inputs "/bin/samtools"))) + ;; This is the easiest way to access the data + ;; needed for the test suite. + (symlink (string-append "../wfmash-v" #$version "/data") + "data") + (and + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-n" "10" "-T" "wflign_info." + "-u" "./"))) + (invoke "head" "LPA.subset.paf"))) + #~()) + ;; This test takes about 5 hours on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.sam" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-N" "-a" "-T" "wflign_info."))) + (with-output-to-file "LPA.subset.sam-view" + (lambda _ + (invoke samtools "view" "LPA.subset.sam" "-bS"))) + (with-output-to-file "LPA.subset.bam" + (lambda _ + (invoke samtools "sort" "LPA.subset.sam-view"))) + (invoke samtools "index" "LPA.subset.bam") + ;; samtools view LPA.subset.bam | head | cut -f 1-9 + ;(invoke samtools "view" "LPA.subset.bam") + ;; There should be an easier way to do this with pipes. + (with-output-to-file "LPA.subset.bam-incr1" + (lambda _ + (invoke samtools "view" "LPA.subset.bam"))) + (with-output-to-file "LPA.subset.bam-incr2" + (lambda _ + (invoke "head" "LPA.subset.bam-incr1"))) + (invoke "cut" "-f" "1-9" "LPA.subset.bam-incr2"))) + #~()) + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset, + ;; setting a lower identity threshold (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.p90.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-p" "90" "-n" "10" + "-T" "wflign_info."))) + (invoke "head" "LPA.subset.p90.paf"))) + #~()) + (begin + ;; Test aligning short reads (500 bps) to a reference (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.500bps.sam" + (lambda _ + (invoke "bin/wfmash" + "data/reference.fa.gz" + "data/reads.500bps.fa.gz" + "-s" "0.5k" "-N" "-a"))) + (with-output-to-file "reads.500bps.sam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.sam" "-bS"))) + (with-output-to-file "reads.500bps.bam" + (lambda _ + (invoke samtools "sort" "reads.500bps.sam-view"))) + (invoke samtools "index" "reads.500bps.bam") + (with-output-to-file "reads.500bps.bam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.bam"))) + (invoke "head" "reads.500bps.bam-view")) + (begin + ;; Test with few very short reads (255bps) (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.255bps.paf" + (lambda _ + (invoke "bin/wfmash" + "data/reads.255bps.fa.gz" + "data/reads.255bps.fa.gz" + "-X" "-w" "16"))) + (invoke "head" "reads.255bps.paf")))))))))) + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (native-inputs + (list samtools)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +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))) |