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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages gkrellm)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages xorg))

(define-public gkrellm
  (package
    (name "gkrellm")
    (version "2.3.5")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://members.dslextreme.com/users/billw/gkrellm/gkrellm-"
                          version ".tar.bz2"))
      (sha256
       (base32
        "12rc6zaa7kb60b9744lbrlfkxxfniprm6x0mispv63h4kh75navh"))))
    (build-system gnu-build-system)
    (inputs
     `(("gettext" ,gnu-gettext)
       ("gtk+" ,gtk+-2)
       ("libice" ,libice)
       ("libsm" ,libsm)))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (arguments
     `(#:tests? #f ; there is no check target
       #:phases
       (alist-delete
        'configure
        %standard-phases)
       #:make-flags
       (let ((out (assoc-ref %outputs "out")))
         (list (string-append "INSTALLROOT=" out)
               "CC=gcc"
               "X11_LIBS = -lX11 -lSM -lICE -lgmodule-2.0"))))
    (home-page "http://members.dslextreme.com/users/billw/gkrellm/gkrellm.html")
    (synopsis "System monitors")
    (description
     "GKrellM is a single process stack of system monitors which supports
applying themes to match its appearance to your window manager, Gtk, or any
other theme.")
    (license license:gpl3+)))
#:use-module (gnu packages jupyter) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) #:use-module (gnu packages logging) #:use-module (gnu packages lsof) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages node) #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) #:use-module (gnu packages parallel) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) #:use-module (gnu packages perl-web) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages rpc) #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages skribilo) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages swig) #:use-module (gnu packages tbb) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) #:use-module (gnu packages textutils) #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages video) #:use-module (gnu packages vim) #:use-module (gnu packages web) #: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)) (define-public aragorn (package (name "aragorn") (version "1.2.41") (source (origin (method url-fetch) (uri (string-append "https://www.ansikte.se/ARAGORN/Downloads/" "aragorn" version ".c")) (sha256 (base32 "0jkzx7sqiarydvz3bwaxh790fpvpkfc926dhsza1dbdhq32ir8wj")))) (build-system gnu-build-system) (arguments (list #:tests? #f ; there are no tests #:phases #~(modify-phases %standard-phases (delete 'configure) (replace 'build (lambda _ (invoke "gcc" "-O3" "-ffast-math" "-finline-functions" "-o" "aragorn" #$source))) (replace 'install (lambda* (#:key inputs #:allow-other-keys) (let ((bin (string-append #$output "/bin")) (man (string-append #$output "/share/man/man1"))) (install-file "aragorn" bin) (mkdir-p man) (copy-file (assoc-ref inputs "aragorn.1") (string-append man "/aragorn.1")))))))) (native-inputs `(("aragorn.1" ,(origin (method url-fetch) (uri "https://www.ansikte.se/ARAGORN/Downloads/aragorn.1") (sha256 (base32 "0bn9lapa6f0cl07dbn2fjrapirv9d4bk7w248w39fhb4vbczcc3f")))))) (home-page "https://www.ansikte.se/ARAGORN/") (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") (description "Aragorn identifies transfer RNA, mitochondrial RNA and transfer-messenger RNA from nucleotide sequences, based on homology to known tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.") (license license:gpl3+))) (define-public bamtools (package (name "bamtools") (version "2.5.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/pezmaster31/bamtools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "14lw571vbks138i0lj66qjdbk8iwa817x2zbpzij61vv1gdgfbn5")))) (build-system cmake-build-system) (arguments (list #:configure-flags '(list "-DBUILD_SHARED_LIBS=ON"))) (inputs (list jsoncpp zlib)) (native-inputs (list pkg-config)) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") (description "BamTools provides both a C++ API and a command-line toolkit for handling BAM files.") (license license:expat))) (define-public bamutils (package (name "bamutils") (version "1.0.15") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/statgen/bamUtil") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1pxydf9qsr8667jh525bc2wiqn9nwk8rkg05kbyfmjs8d261fl9y")))) (build-system gnu-build-system) (arguments (list #:tests? #f ;fails to link debug libraries #:test-target "test" #:make-flags #~(list (string-append "INSTALLDIR=" #$output "/bin")) #:phases #~(modify-phases %standard-phases (replace 'configure (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makefile" (("^DATE=.*") "DATE=\"1970-01-01\"\n")) (copy-recursively (assoc-ref inputs "libstatgen") "../libStatGen")))))) (inputs (list zlib)) (native-inputs `(("libstatgen" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/statgen/libStatGen/") (commit (string-append "v" version)))) (file-name (git-file-name "libstatgen" version)) (sha256 (base32 "0spvbpvnpxrgj8kajpkhf1mv7kdyvj723y9zh13jykvnjh8a15j3")))))) (home-page "https://genome.sph.umich.edu/wiki/BamUtil") (synopsis "Programs for working on SAM/BAM files") (description "This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called @code{bam}.") (license license:gpl3+))) (define-public bcftools (package (name "bcftools") (version "1.14") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" "releases/download/" version "/bcftools-" version ".tar.bz2")) (sha256 (base32 "1jqrma16fx8kpvb3c0462dg0asvmiv5yi8myqmc5ddgwi6p8ivxp")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. (delete-file-recursively "htslib-1.14"))))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-libgsl") #:test-target "test" #:phases (modify-phases %standard-phases (add-before 'check 'patch-tests (lambda _ (substitute* "test/test.pl" (("/bin/bash") (which "bash")))))))) (native-inputs (list htslib perl)) (inputs (list gsl zlib)) (home-page "https://samtools.github.io/bcftools/") (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") (description "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) (define-public bcftools-1.12 (package/inherit bcftools (version "1.12") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" "releases/download/" version "/bcftools-" version ".tar.bz2")) (sha256 (base32 "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. (delete-file-recursively "htslib-1.12"))))) (native-inputs (list htslib-1.12 perl)))) (define-public bcftools-1.10 (package/inherit bcftools (version "1.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" "releases/download/" version "/bcftools-" version ".tar.bz2")) (sha256 (base32 "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. (delete-file-recursively "htslib-1.10"))))) (native-inputs (list htslib-1.10 perl)))) (define-public bedops (package (name "bedops") (version "2.4.41") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bedops/bedops") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l")))) (build-system gnu-build-system) (arguments (list ;; We cannot run the tests because the build system makes strange ;; assumptions about where executables are located. #:tests? #false #:test-target "tests" #:make-flags #~(list (string-append "CC=" #$(cc-for-target))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'unpack-tarballs (lambda _ ;; FIXME: Bedops includes tarballs of minimally patched upstream ;; libraries jansson, zlib, and bzip2. We cannot just use stock ;; libraries because at least one of the libraries (zlib) is ;; patched to add a C++ function definition (deflateInit2cpp). ;; Until the Bedops developers offer a way to link against system ;; libraries we have to build the in-tree copies of these three ;; libraries. ;; See upstream discussion: ;; https://github.com/bedops/bedops/issues/124 ;; Unpack the tarballs to benefit from shebang patching. (with-directory-excursion "third-party" (invoke "tar" "xvf" "jansson-2.6.tar.bz2") (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2") (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2")) ;; Disable unpacking of tarballs in Makefile. (substitute* "system.mk/Makefile.linux" (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") (("\\./configure") "CONFIG_SHELL=bash ./configure")) (substitute* "third-party/zlib-1.2.7/Makefile.in" (("^SHELL=.*$") "SHELL=bash\n")))) (delete 'configure) (replace 'install (lambda _ (invoke "make" "install" (string-append "BINDIR=" #$output "/bin"))))))) (native-inputs (list diffutils perl which)) (home-page "https://github.com/bedops/bedops") (synopsis "Tools for high-performance genomic feature operations") (description "BEDOPS is a suite of tools to address common questions raised in genomic studies---mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. BEDOPS provides tools that perform highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.") (license license:gpl2+))) (define-public bedtools (package (name "bedtools") (version "2.30.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/releases/" "download/v" version "/" "bedtools-" version ".tar.gz")) (sha256 (base32 "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik")))) (build-system gnu-build-system) (arguments (list #:test-target "test" #:make-flags #~(list (string-append "prefix=" #$output)) #:phases '(modify-phases %standard-phases (delete 'configure)))) (native-inputs (list python-wrapper)) (inputs (list samtools zlib)) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") (description "Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:expat))) ;; Later releases of bedtools produce files with more columns than ;; what Ribotaper expects. (define-public bedtools-2.18 (package (inherit bedtools) (name "bedtools") (version "2.18.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/" "releases/download/v" version "/bedtools-" version ".tar.gz")) (sha256 (base32 "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz")))) (arguments (list #:test-target "test" #:phases #~(modify-phases %standard-phases (add-after 'unpack 'compatibility (lambda _ (substitute* "src/utils/fileType/FileRecordTypeChecker.h" (("static const float PERCENTAGE") "static constexpr float PERCENTAGE")) (substitute* "src/utils/general/DualQueue.h" (("template <class T, template<class T> class CompareFunc>") "template <class T, template<class U> class CompareFunc>")) (substitute* '("src/utils/BamTools/src/api/algorithms/Sort.h" "src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h") (("(bool operator\\(\\).*) \\{" m pre) (string-append pre " const {"))))) (delete 'configure) (replace 'install (lambda _ (let ((bin (string-append #$output "/bin/"))) (for-each (lambda (file) (install-file file bin)) (find-files "bin" ".*")))))))) (native-inputs (list python-wrapper)) (inputs (list samtools zlib)))) (define-public bitmapperbs (package (name "bitmapperbs") (version "1.0.2.3") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/chhylp123/BitMapperBS/") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v")) (modules '((guix build utils))) ;; This package bundles a modified copy of htslib, so we cannot ;; unbundle it. (snippet '(begin (delete-file-recursively "libdivsufsort-2.0.1") (delete-file-recursively "pSAscan-0.1.0"))))) (build-system gnu-build-system) (arguments (list #:tests? #false #:make-flags '(list "bitmapperBS") ;; The build system checks for CPU features. For this reason, we want ;; users to build it locally instead of using substitutes. #:substitutable? #false #:phases #~(modify-phases %standard-phases (add-after 'unpack 'fix-build-system (lambda _ (substitute* "Makefile" (("make prefix=../htslib_aim install") (string-append "make prefix=" #$output " install-so")) (("htslib_aim/include") "htslib") (("htslib_aim/lib") (string-append #$output "/lib"))))) (add-after 'unpack 'patch-references-to-psascan (lambda* (#:key inputs #:allow-other-keys) (substitute* "Makefile" (("\"(./)?psascan" pre all) (string-append "\"" pre (search-input-file inputs "/bin/psascan")))))) (delete 'configure) (replace 'install (lambda _ (install-file "bitmapperBS" (string-append #$output "/bin/"))))))) (inputs (list libdivsufsort psascan zlib)) (home-page "https://github.com/chhylp123/BitMapperBS/") (synopsis "Read aligner for whole-genome bisulfite sequencing") (description "BitMapperBS is memory-efficient aligner that is designed for whole-genome bisulfite sequencing (WGBS) reads from directional protocol.") (supported-systems '("x86_64-linux")) (license license:asl2.0))) (define-public bustools (package (name "bustools") (version "0.43.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/BUStools/bustools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "068kjlc4d528269nl5mc3j8h2c95r1v545d3fi1iw1ckg8rba0hg")))) (build-system cmake-build-system) (arguments (list #:tests? #f)) ;no test target (inputs (list zlib)) (home-page "https://bustools.github.io") (synopsis "Tools for working with BUS files") (description "bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.") (license license:bsd-2))) (define-public cellsnp-lite ;; Last release is from November 2021 and does not contain fixes. (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") (revision "0")) (package (name "cellsnp-lite") (version (git-version "1.2.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/single-cell-genetics/cellsnp-lite") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444")))) (build-system gnu-build-system) (arguments (list #:configure-flags #~(list (string-append "--with-htslib=" #$(this-package-input "htslib"))))) (inputs (list curl htslib openssl zlib)) (native-inputs (list autoconf)) (home-page "https://cellsnp-lite.readthedocs.io") (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data") (description "This package is designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with other packages, which assigns cells to donors and detects doublets as vireo, even without genotyping reference. This package is the C version of the deprecated cellSNP implemented in Python. Compared to cellSNP, this package is more efficient with higher speed and less memory usage.") (license license:asl2.0)))) (define-public cpat (package (name "cpat") (version "3.0.4") (source (origin (method url-fetch) (uri (pypi-uri "CPAT" version)) (sha256 (base32 "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd")) (modules '((guix build utils))) (snippet '(for-each delete-file-recursively (list ".eggs" "lib/__pycache__/" "lib/cpmodule/__pycache__/"))))) (build-system pyproject-build-system) (arguments (list #:phases '(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (with-directory-excursion "test" ;; There is no test4.fa (substitute* "test.sh" ((".*-g test4.fa.*") "")) (invoke "bash" "test.sh")))))))) (propagated-inputs (list python-numpy python-pysam)) (inputs (list r-minimal)) (home-page "https://wlcb.oit.uci.edu/cpat/") (synopsis "Alignment-free distinction between coding and noncoding RNA") (description "CPAT is a method to distinguish coding and noncoding RNA by using a logistic regression model based on four pure sequence-based, linguistic features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias. Linguistic features based method does not require other genomes or protein databases to perform alignment and is more robust. Because it is alignment-free, it runs much faster and also easier to use.") (license license:gpl2+))) (define-public pbcopper (package (name "pbcopper") (version "2.0.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/pbcopper") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "04mgmla96bsmr9gijbn3ibspry625cv4kqqxv70z4jq4qc407jy3")))) (build-system meson-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-meson-files (lambda _ (substitute* "meson.build" (("-msse4.1") ""))))))) (inputs (list boost)) (native-inputs (list googletest pkg-config)) (home-page "https://github.com/PacificBiosciences/pbcopper") (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications") (description "The pbcopper library provides a suite of data structures, algorithms, and utilities for PacBio C++ applications.") (license license:bsd-3))) (define-public r-anndatar (let ((commit "5c3eb7e498d0d9bf1c522ad66f4eb8ad277238b6") (revision "1")) (package (name "r-anndatar") (version (git-version "0.99.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/scverse/anndataR") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0sx87i8cb4p08ihgpgflxs0fhkr1kw6lxvky4w766rq7wqy41cgk")))) (properties `((upstream-name . "anndataR"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/scverse/anndataR") (synopsis "AnnData interoperability in R") (description "This package aims to bring the power and flexibility of @code{AnnData} to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into @code{SingleCellExperiment} and Seurat objects.") (license license:expat)))) (define-public r-anpan (let ((commit "286b88dcf5e9e963a595482139aade154ee1dc86") (revision "1")) (package (name "r-anpan") (version (git-version "0.3.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/biobakery/anpan") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "10nw5v69gn4pxb4g5gd8nh9r1ywd6yczapl3dpdfms0434wcmkxm")))) (properties `((upstream-name . "anpan"))) (build-system r-build-system) (propagated-inputs (list r-ape r-cmdstanr r-data-table r-dplyr r-fastglm r-furrr r-future r-ggdendro r-ggnewscale r-ggplot2 r-loo r-mass r-patchwork r-phylogram r-posterior r-progressr r-purrr r-r-utils r-stringr r-tibble r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/biobakery/anpan") (synopsis "Quantifying microbial strain-host associations") (description "The goal of anpan is to consolidate statistical methods for strain analysis. This includes automated filtering of metagenomic functional profiles, testing genetic elements for association with outcomes, phylogenetic association testing, and pathway-level random effects models.") (license license:expat)))) (define-public r-bedtorch (let ((commit "f5ff4f83b94f59eac660333c64e4b2f296b35cea") (revision "1")) (package (name "r-bedtorch") (version (git-version "0.1.12.12" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/haizi-zh/bedtorch/") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "08l04iqf54b5995gc7rvqqd7w327fwqs7qjyhc9y5cqfj8yv4c48")))) (properties `((upstream-name . "bedtorch"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-curl r-data-table r-dplyr r-genomeinfodb r-genomicranges r-purrr r-r-utils r-rcpp r-rcurl r-readr r-rhtslib12 r-s4vectors r-stringr r-tidyr)) (home-page "https://github.com/haizi-zh/bedtorch/") (synopsis "R package for fast BED-file manipulation") (description "The goal of bedtorch is to provide a fast BED file manipulation tool suite native in R.") (license license:expat)))) (define-public r-bpcells (let ((commit "32ce67312185d3ed1046b4218dd3aaf1b35dcfda") (revision "1")) (package (name "r-bpcells") (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bnprks/BPCells/") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0im4sqvbii326acmd1hnimyzsllnbvnh9al3dp1nla6isgi7s6cg")))) (properties `((upstream-name . "BPCells"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'do-not-tune (lambda _ (substitute* "configure" (("\"-march=native\"") "\"\""))))))) (inputs (list hdf5 zlib)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-hexbin r-magrittr r-matrix r-patchwork r-rcolorbrewer r-rcpp r-rcppeigen r-rlang r-scales r-scattermore r-stringr r-tibble r-tidyr r-vctrs)) (native-inputs (list pkg-config)) (home-page "https://github.com/bnprks/BPCells/") (synopsis "Single cell counts matrices to PCA") (description "This is a package providing efficient operations for single cell ATAC-seq fragments and RNA counts matrices. It is interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.") (license license:gpl3)))) (define-public r-btools (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") (revision "1")) (package (name "r-btools") (version (git-version "0.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/twbattaglia/btools") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0bca593dnxz6xdywpdi0ipli0paln2b3bfxxj0csnmj55ryrz428")))) (properties `((upstream-name . "btools"))) (build-system r-build-system) (propagated-inputs (list r-biomformat r-coin r-deseq2 r-dplyr r-genefilter r-phyloseq r-picante r-plotly r-reshape2 r-stringr r-vegan)) (home-page "https://github.com/twbattaglia/btools") (synopsis "R functions for microbial diversity analyses") (description "This package provides an assortment of R functions that is suitable for all types of microbial diversity analyses.") (license license:expat)))) (define-public r-codeandroll2 (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f") (revision "1")) (package (name "r-codeandroll2") (version (git-version "2.3.6" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/vertesy/CodeAndRoll2") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71")))) (properties `((upstream-name . "CodeAndRoll2"))) (build-system r-build-system) (propagated-inputs (list r-colorramps r-dplyr r-gplots r-gtools r-plyr r-rcolorbrewer r-sessioninfo r-sm r-stringendo r-stringr)) (home-page "https://github.com/vertesy/CodeAndRoll2") (synopsis "CodeAndRoll2 for vector, matrix and list manipulations") (description "CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.") (license license:gpl3)))) (define-public r-conospanel (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9") (revision "1")) (package (name "r-conospanel") (version (git-version "1.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/kharchenkolab/conosPanel") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1zf0aj5d4iaxc3ghvjnaja5qby1avlmljzh94bpyvxbd359z9snn")))) (properties `((upstream-name . "conosPanel"))) (build-system r-build-system) (home-page "https://github.com/kharchenkolab/conosPanel") (synopsis "Data for the conos package") (description "The data within this package is a panel of four samples, each with 3000 cells. There are two samples which are bone marrow (BM), and two samples which are cord blood (CB).") (license license:gpl3)))) (define-public r-conqur (let ((commit "c7a88794efd4ecfe4d96988dceeec3b410222e48") (revision "1")) (package (name "r-conqur") (version (git-version "2.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/wdl2459/ConQuR") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "19a7p2l67mgjy99i5ksjxlhzaqmrnyi1vzvwnhgnx2jrr6crj7rq")))) (properties `((upstream-name . "ConQuR"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-compositions r-cqrreg r-doparallel r-dplyr r-fastdummies r-glmnet r-gplots r-gunifrac r-quantreg r-randomforest r-rocr r-vegan)) (native-inputs (list r-knitr)) (home-page "https://github.com/wdl2459/ConQuR") (synopsis "Batch effects removal for microbiome data") (description "This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.") (license license:gpl3)))) (define-public r-ewastools (let ((commit "f7646cacd73266708479b3fea5d625054d179f95") (revision "1")) (package (name "r-ewastools") (version (git-version "1.7.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/hhhh5/ewastools/") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41")))) (properties `((upstream-name . "ewastools"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-igraph r-illuminaio r-mblm r-quadprog)) (native-inputs (list r-knitr)) (home-page "https://github.com/hhhh5/ewastools/") (synopsis "Quality control toolset for the Illumina Infinium DNA methylation") (description "This package provides a collection of useful functions for working with DNA methylation micro-array data.") (license license:unlicense)))) (define-public r-numbat (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295") (revision "1")) (package (name "r-numbat") (version (git-version "1.3.2-1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/kharchenkolab/numbat") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0wa2cz5iy570r2a57bd74jramxayvfhmxznb0vq4vyk1ia8l5jd1")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape r-catools r-data-table r-dendextend r-dplyr r-genomicranges r-ggplot2 r-ggraph r-ggtree r-glue r-igraph r-iranges r-logger r-magrittr r-matrix r-optparse r-paralleldist r-patchwork r-pryr r-purrr r-r-utils r-rcpp r-rcpparmadillo r-rhpcblasctl r-roptim r-scales r-scistreer r-stringr r-tibble r-tidygraph r-tidyr r-vcfr r-zoo)) (home-page "https://github.com/kharchenkolab/numbat") (synopsis "Haplotype-Aware CNV Analysis from scRNA-Seq") (description "This package provides a computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. numbat integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. numbat can be used to: @enumerate @item detect allele-specific copy number variations from single-cells; @item differentiate tumor versus normal cells in the tumor microenvironment; @item infer the clonal architecture and evolutionary history of profiled tumors. @end enumerate numbat does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output).") (license license:expat)))) (define-public r-p2data (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c") (revision "1")) (package (name "r-p2data") (version (git-version "1.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/kharchenkolab/p2data") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1hadrldldxvhqs43aqs3c88bqfgql3wcfkbll3jz7fh6z7p3x324")))) (properties `((upstream-name . "p2data"))) (build-system r-build-system) (home-page "https://github.com/kharchenkolab/p2data") (synopsis "Data for pagoda2") (description "This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.") (license license:gpl3)))) (define-public r-rhtslib12 (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30") (revision "1")) (package (name "r-rhtslib12") (version (git-version "1.23.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/haizi-zh/Rhtslib12") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0a3kkp0phi2fq6ip8p9vfj3axn7l15f2mb51a6v3ai4nlkhqqawj")))) (properties `((upstream-name . "Rhtslib12"))) (build-system r-build-system) (propagated-inputs (list curl zlib r-zlibbioc)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/haizi-zh/Rhtslib12") (synopsis "HTSlib high-throughput sequencing library as an R package") (description "This package provides version 1.12 of the HTSlib C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) (define-public r-scenic (let ((commit "cedf8490a634da550cea2c831544e5f7f14467d2") (revision "1")) (package (name "r-scenic") (version (git-version "1.3.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/SCENIC") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "17ai0q260hdqbvm1km1s5dw93pgz4f546ycfii57jyy9m9jka7r0")))) (properties `((upstream-name . "SCENIC"))) (build-system r-build-system) (propagated-inputs (list r-aucell r-data-table r-dynamictreecut r-genie3 r-ggrepel r-mixtools r-nmf r-rcistarget r-rtsne)) (native-inputs (list r-knitr)) (home-page "https://github.com/aertslab/SCENIC") (synopsis "SCENIC (Single Cell rEgulatory Network Inference and Clustering)") (description "SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.") ;; As of commit cedf8490a634da550cea2c831544e5f7f14467d2 the license is ;; GPLv3. (license license:gpl3)))) (define-public r-scent (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5") (revision "1")) (package (name "r-scent") (version (git-version "1.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/immunogenomics/SCENT") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi")))) (properties `((upstream-name . "SCENT"))) (build-system r-build-system) (inputs (list bedtools)) (propagated-inputs (list r-boot r-data-table r-hmisc r-lme4 r-mass r-matrix r-r-utils r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/immunogenomics/SCENT") (synopsis "Single-Cell enhancer target gene mapping for multimodal single-cell data") (description "This package contains functions for the SCENT algorithm. SCENT uses single-cell multimodal data and links ATAC-seq peaks to their target genes by modeling association between chromatin accessibility and gene expression across individual single cells.") (license license:expat)))) (define-public r-saige (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167") (revision "1")) (package (name "r-saige") (version (git-version "1.3.4" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/saigegit/SAIGE") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0c3211whqazycs9ivwdz23imj45j4na2xzcfq5l989ykkgmqnjzs")))) (properties `((upstream-name . "SAIGE"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'do-not-download-packages (lambda _ ;; Pretend to be a Conda build to avoid having to install ;; things with pip and cget. (setenv "CONDA_BUILD" "1"))) (add-after 'unpack 'link-with-openblas (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makevars" (("-llapack") (search-input-file inputs "/lib/libopenblas.so")))))))) (inputs (list openblas savvy superlu zlib zstd)) (propagated-inputs (list r-bh r-data-table r-dplyr r-matrix r-metaskat r-optparse r-qlcmatrix r-rcpp r-rcpparmadillo r-rcppeigen r-rcppparallel r-rhpcblasctl r-rsqlite r-skat r-spatest)) (home-page "https://github.com/saigegit/SAIGE") (synopsis "Genome-wide association tests in large-scale data sets") (description "SAIGE is a package for efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+).") (license license:gpl2+)))) (define-public r-singlet (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36") (revision "1")) (package (name "r-singlet") (version (git-version "0.99.26" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/zdebruine/singlet") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "040v8wzl9qr8ribr6qss61fz4698d14cqs8nxbc8hqwiqlpy3vs4")))) (properties `((upstream-name . "singlet"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-fgsea r-ggplot2 r-knitr r-limma r-matrix r-msigdbr r-rcpp r-rcppml/devel r-reshape2 r-scuttle r-seurat)) (native-inputs (list r-knitr)) (home-page "https://github.com/zdebruine/singlet") (synopsis "Non-negative Matrix Factorization for single-cell analysis") (description "This is a package for fast @dfn{Non-negative Matrix Factorization} (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.") (license license:gpl2+)))) (define-public r-stacas (package (name "r-stacas") (version "2.2.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/carmonalab/STACAS") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm")))) (properties `((upstream-name . "STACAS"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors r-biocparallel r-ggplot2 r-ggridges r-pbapply r-r-utils r-seurat)) (home-page "https://github.com/carmonalab/STACAS") (synopsis "Sub-type anchoring correction for alignment in Seurat") (description "This package implements methods for batch correction and integration of scRNA-seq datasets, based on the Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogenous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of the package allows the users to incorporate explicit information about cell-types in order to assist the integration process.") (license license:gpl3))) (define-public r-stringendo (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a") (revision "1")) (package (name "r-stringendo") (version (git-version "0.6.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/vertesy/Stringendo") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "15ij4zf2j9c8m9n4bqhmxkchjh2bhddwjfxngfpwv7c5wjqyi6ir")))) (properties `((upstream-name . "Stringendo"))) (build-system r-build-system) (propagated-inputs (list r-clipr)) (home-page "https://github.com/vertesy/Stringendo") (synopsis "Stringendo is a string parsing library") (description "This package provides string parsing functionalites for generating plotnames, filenames and paths.") (license license:gpl3)))) (define-public r-readwriter (let ((commit "91373c44641014a1ce8e1c3e928747608aae8f54") (revision "1")) (package (name "r-readwriter") (version (git-version "1.5.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/vertesy/ReadWriter") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "156kvmplrip0w1zhs9yl5r0ayjipa0blhy614l65hbsjn1lwbskr")))) (properties `((upstream-name . "ReadWriter"))) (build-system r-build-system) (propagated-inputs (list r-gtools r-openxlsx r-readr r-stringendo)) (home-page "https://github.com/vertesy/ReadWriter") (synopsis "Functions to read and write files conveniently") (description "ReadWriter is a set of R functions to read and write files conveniently.") (license license:gpl3)))) (define-public r-streamgraph (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") (revision "1")) (package (name "r-streamgraph") (version (git-version "0.9.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/hrbrmstr/streamgraph") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "010rhnby5a9dg08jvlkr65b3p9iipdxi2f5m1k6j53s80p25yvig")))) (properties `((upstream-name . "streamgraph"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-htmltools r-htmlwidgets r-magrittr r-tidyr r-xts)) (native-inputs (list r-knitr)) (home-page "https://github.com/hrbrmstr/streamgraph") (synopsis "Htmlwidget for building streamgraph visualizations") (description "A streamgraph is a type of stacked area chart. It represents the evolution of a numeric variable for several groups. Areas are usually displayed around a central axis, and edges are rounded to give a flowing shape. This package provides an @code{htmlwidget} for building streamgraph visualizations.") (license license:expat)))) (define-public r-wasabi (let ((commit "8c33cabde8d18c2657cd6e38e7cb834f87cf9846") (revision "1")) (package (name "r-wasabi") (version (git-version "1.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/COMBINE-lab/wasabi") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0rpdj6n4cnx8n2zl60dzgl638474sg49dknwi9x3qb4g56dpphfa")))) (properties `((upstream-name . "wasabi"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-rhdf5 r-rjson)) (home-page "https://github.com/COMBINE-lab/wasabi") (synopsis "Use Sailfish and Salmon with Sleuth") (description "This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.") (license license:bsd-3)))) (define-public pbbam (package (name "pbbam") (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/pbbam") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc")))) (build-system meson-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-tests (lambda* (#:key inputs #:allow-other-keys) ;; Disable this test. I tried fixing it by including ;; optional_io.hpp, but there's a type error. (substitute* "tests/src/meson.build" (("'test_ReadGroupInfo.cpp',") "")) #; (substitute* "include/pbbam/ReadGroupInfo.h" (("#include <boost/optional.hpp>" m) (string-append m "\n#include <boost/optional/optional_io.hpp>"))) (substitute* '("tests/scripts/cram/_test.py" "tests/scripts/cram/_main.py") (("'/bin/sh'") (string-append "'" (which "sh") "'")))))))) ;; These libraries are listed as "Required" in the pkg-config file. (propagated-inputs (list htslib-1.14 pbcopper zlib)) (inputs (list boost samtools)) (native-inputs (list googletest pkg-config python-wrapper)) ;for tests (home-page "https://github.com/PacificBiosciences/pbbam") (synopsis "Work with PacBio BAM files") (description "The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. This library is not intended to be used as a general-purpose BAM utility - all input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (license license:bsd-3))) (define-public pbgzip (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) (package (name "pbgzip") (version (git-version "0.0.0" "0" commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/nh13/pbgzip") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) (build-system gnu-build-system) (native-inputs (list autoconf automake)) (inputs (list zlib)) (home-page "https://github.com/nh13/pbgzip") (synopsis "Parallel Block GZIP") (description "This package implements parallel block gzip. For many formats, in particular genomics data formats, data are compressed in fixed-length blocks such that they can be easily indexed based on a (genomic) coordinate order, since typically each block is sorted according to this order. This allows for each block to be individually compressed (deflated), or more importantly, decompressed (inflated), with the latter enabling random retrieval of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited to any particular format, but certain features are tailored to genomics data formats when enabled. Parallel decompression is somewhat faster, but the true speedup comes during compression.") (license license:expat)))) (define-public blasr-libcpp (package (name "blasr-libcpp") (version "5.3.5") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/blasr_libcpp") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "07cdfnfl29zf2j7fpaaqaxghq3p0wnc109razs0icwm2q6l3gycb")))) (build-system meson-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'link-with-hdf5 (lambda* (#:key inputs #:allow-other-keys) (let ((hdf5 (assoc-ref inputs "hdf5"))) (substitute* "meson.build" (("libblasr_deps = \\[" m) (string-append m (format #f "cpp.find_library('hdf5', dirs : '~a'), \ cpp.find_library('hdf5_cpp', dirs : '~a'), " hdf5 hdf5))))))) (add-after 'unpack 'find-googletest (lambda* (#:key inputs #:allow-other-keys) ;; It doesn't find gtest_main because there's no pkg-config file ;; for it. Find it another way. (substitute* "unittest/meson.build" (("libblasr_gtest_dep = dependency\\('gtest_main'.*") (format #f "cpp = meson.get_compiler('cpp') libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" (assoc-ref inputs "googletest"))))))) ;; TODO: unittest/libblasr_unittest cannot be linked ;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o: ;; undefined reference to symbol ;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_' ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so: ;; error adding symbols: DSO missing from command line #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs (list boost hdf5 htslib pbbam zlib)) (native-inputs (list googletest pkg-config)) (home-page (string-append "https://web.archive.org/web/20201106122415/" "https://github.com/PacificBiosciences/blasr_libcpp")) (synopsis "Library for analyzing PacBio genomic sequences") (description "This package provides three libraries used by applications for analyzing PacBio genomic sequences. This library contains three sub-libraries: pbdata, hdf and alignment.") (license license:bsd-3))) (define-public blasr (package (name "blasr") (version "5.3.5") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/blasr") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "0axyd06gn2xa0p0k76fihsbxpfxvhlb18jn6bf97c0ii58r1wc0k")))) (build-system meson-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'link-with-hdf5 (lambda* (#:key inputs #:allow-other-keys) (let ((hdf5 (assoc-ref inputs "hdf5"))) (substitute* "meson.build" (("blasr_deps = \\[" m) (string-append m (format #f "cpp.find_library('hdf5', dirs : '~a'), \ cpp.find_library('hdf5_cpp', dirs : '~a'), " hdf5 hdf5)))))))) ;; Tests require "cram" executable, which is not packaged. #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs (list boost blasr-libcpp hdf5 pbbam zlib)) (native-inputs (list pkg-config)) (home-page (string-append "https://web.archive.org/web/20210813124135/" "https://github.com/PacificBiosciences/blasr")) (synopsis "PacBio long read aligner") (description "Blasr is a genomic sequence aligner for processing PacBio long reads.") (license license:bsd-3))) (define-public randfold (package (name "randfold") (version "2.0.1") (source (origin (method url-fetch) (uri (string-append "http://bioinformatics.psb.ugent.be/" "supplementary_data/erbon/nov2003/downloads/" &qu