diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 359 |
1 files changed, 302 insertions, 57 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 002b417b54..0b87d37bcf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -388,10 +388,10 @@ 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-1.9 +(define-public bcftools-1.10 (package (inherit bcftools) (name "bcftools") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" @@ -399,15 +399,15 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.10") #t)))) (build-system gnu-build-system) (native-inputs - `(("htslib" ,htslib-1.9) + `(("htslib" ,htslib-1.10) ("perl" ,perl))))) (define-public bedops @@ -1213,14 +1213,14 @@ sequencing.") (define-public python-biopython (package (name "python-biopython") - (version "1.70") + (version "1.73") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) (build-system python-build-system) (arguments `(#:phases @@ -2043,7 +2043,7 @@ has several key features: (define-public python-pysam (package (name "python-pysam") - (version "0.15.1") + (version "0.16.0.1") (source (origin (method git-fetch) ;; Test data is missing on PyPi. @@ -2053,7 +2053,7 @@ has several key features: (file-name (git-file-name name version)) (sha256 (base32 - "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) + "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f")) (modules '((guix build utils))) (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools @@ -2073,36 +2073,37 @@ has several key features: (setenv "LDFLAGS" "-lncurses") (setenv "CFLAGS" "-D_CURSES_LIB=1"))) (replace 'check - (lambda _ - ;; This file contains tests that require a connection to the - ;; internet. - (delete-file "tests/tabix_test.py") + (lambda* (#:key tests? #:allow-other-keys) ;; FIXME: These tests fail with "AttributeError: 'array.array' ;; object has no attribute 'tostring'". (delete-file "tests/AlignmentFile_test.py") - (delete-file "tests/AlignedSegment_test.py") - ;; Step out of source dir so python does not import from CWD. - (with-directory-excursion "tests" - (setenv "HOME" "/tmp") - (invoke "make" "-C" "pysam_data") - (invoke "make" "-C" "cbcf_data") - ;; Running nosetests without explicitly asking for a single - ;; process leads to a crash. Running with multiple processes - ;; fails because the tests are not designed to run in parallel. - - ;; FIXME: tests keep timing out on some systems. - (invoke "nosetests" "-v" "--processes" "1"))))))) + (when tests? + ;; Step out of source dir so python does not import from CWD. + (with-directory-excursion "tests" + (setenv "HOME" "/tmp") + (invoke "make" "-C" "pysam_data") + (invoke "make" "-C" "cbcf_data") + (invoke "pytest" "-k" + (string-append + ;; requires network access. + "not FileHTTP" + ;; bug in test suite with samtools update + ;; https://github.com/pysam-developers/pysam/issues/961 + " and not TestHeaderBAM" + " and not TestHeaderCRAM" + " and not test_text_processing"))))))))) (propagated-inputs - `(("htslib" ,htslib-1.9))) ; Included from installed header files. + `(("htslib" ,htslib-1.10))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("curl" ,curl) ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) ;; Dependencies below are are for tests only. - ("samtools" ,samtools-1.9) - ("bcftools" ,bcftools-1.9) + ("samtools" ,samtools-1.10) + ("bcftools" ,bcftools-1.10) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") @@ -3589,7 +3590,7 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) - ("seqan" ,seqan))) + ("seqan" ,seqan-2))) (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description @@ -4603,6 +4604,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.10 + (package (inherit htslib) + (name "htslib") + (version "1.10") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "0wm9ay7qgypj3mwx9zl1mrpnr36298b1aj5vx69l4k7bzbclvr3s")))))) + (define-public htslib-1.9 (package (inherit htslib) (name "htslib") @@ -6051,10 +6065,10 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) -(define-public samtools-1.9 +(define-public samtools-1.10 (package (inherit samtools) (name "samtools") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) @@ -6063,14 +6077,14 @@ viewer.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.10") #t)))) (inputs - `(("htslib" ,htslib-1.9) + `(("htslib" ,htslib-1.10) ("ncurses" ,ncurses) ("perl" ,perl) ("python" ,python) @@ -6706,6 +6720,39 @@ writing files into the .sra format.") (define-public seqan (package (name "seqan") + (version "3.0.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/seqan/seqan3/releases/" + "download/" version "/seqan3-" + version "-Source.tar.xz")) + (sha256 + (base32 + "1h2z0cvgidhkmh5xsbw75waqbrqbbv6kkrvb0b92xfh3gqpaiz22")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "ctest" "test" "--output-on-failure")))))) + (native-inputs + `(("bzip2" ,bzip2) + ("cereal" ,cereal) + ("zlib" ,zlib))) + (home-page "https://www.seqan.de") + (synopsis "Library for nucleotide sequence analysis") + (description + "SeqAn is a C++ library of efficient algorithms and data structures for +the analysis of sequences with the focus on biological data. It contains +algorithms and data structures for string representation and their +manipulation, online and indexed string search, efficient I/O of +bioinformatics file formats, sequence alignment, and more.") + (license license:bsd-3))) + +(define-public seqan-2 + (package + (inherit seqan) (version "2.4.0") (source (origin (method url-fetch) @@ -6737,16 +6784,7 @@ writing files into the .sra format.") (native-inputs `(("source" ,source) ("tar" ,tar) - ("xz" ,xz))) - (home-page "https://www.seqan.de") - (synopsis "Library for nucleotide sequence analysis") - (description - "SeqAn is a C++ library of efficient algorithms and data structures for -the analysis of sequences with the focus on biological data. It contains -algorithms and data structures for string representation and their -manipulation, online and indexed string search, efficient I/O of -bioinformatics file formats, sequence alignment, and more.") - (license license:bsd-3))) + ("xz" ,xz))))) (define-public seqan-1 (package (inherit seqan) @@ -9310,6 +9348,54 @@ using nucleotide or amino-acid sequence data.") ;; GPLv3 only (license license:gpl3))) +(define-public segemehl + (package + (name "segemehl") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (string-append "https://www.bioinf.uni-leipzig.de/Software" + "/segemehl/downloads/segemehl-" + version ".tar.gz")) + (sha256 + (base32 + "0lbzbb7i8zadsn9b99plairhq6s2h1z8qdn6n7djclfis01nycz4")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list (string-append "CC=" ,(cc-for-target)) + "all") + #:tests? #false ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (exes (list "segemehl.x" "haarz.x"))) + (mkdir-p bin) + (for-each (lambda (exe) + (install-file exe bin)) + exes))))))) + (inputs + `(("htslib" ,htslib) + ("ncurses" ,ncurses) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl") + (synopsis "Map short sequencer reads to reference genomes") + (description "Segemehl is software to map short sequencer reads to +reference genomes. Segemehl implements a matching strategy based on enhanced +suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and +bgzip'ed). In addition to the alignment of reads from standard DNA- and +RNA-seq protocols, it also allows the mapping of bisulfite converted +reads (Lister and Cokus) and implements a split read mapping strategy. The +output of segemehl is a SAM or BAM formatted alignment file.") + (license license:gpl3+))) + (define-public kallisto (package (name "kallisto") @@ -12991,28 +13077,32 @@ downstream analysis.") ("taxtastic" ,taxtastic))) (synopsis "Pplacer Python scripts"))) -(define-public python2-checkm-genome +(define-public checkm (package - (name "python2-checkm-genome") - (version "1.0.13") + (name "checkm") + (version "1.1.3") (source (origin (method url-fetch) (uri (pypi-uri "checkm-genome" version)) (sha256 (base32 - "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz")))) + "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz")))) (build-system python-build-system) (arguments - `(#:python ,python-2 - #:tests? #f)) ; some tests are interactive - (propagated-inputs - `(("python-dendropy" ,python2-dendropy) - ("python-matplotlib" ,python2-matplotlib) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-scipy" ,python2-scipy))) - (home-page "https://pypi.org/project/Checkm/") + `(#:tests? #f ; Some tests fail for unknown reasons. + #:phases + (modify-phases %standard-phases + (add-before 'check 'set-HOME + (lambda _ + (setenv "HOME" "/tmp")))))) + (inputs + `(("python-dendropy" ,python-dendropy) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy))) + (home-page "https://ecogenomics.github.io/CheckM/") (synopsis "Assess the quality of putative genome bins") (description "CheckM provides a set of tools for assessing the quality of genomes @@ -13027,6 +13117,9 @@ 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") @@ -14490,3 +14583,155 @@ quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.") (license license:expat)))) + +(define-public tombo + (package + (name "tombo") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ont-tombo" version)) + (sha256 + (base32 + "1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose2" ,python-nose2))) + ;; The package mainly consists of a command-line tool, but also has a + ;; Python-API. Thus these must be propagated. + (propagated-inputs + `(("python-future" ,python-future) + ("python-h5py" ,python-h5py) + ("python-mappy" ,python-mappy) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-tqdm" ,python-tqdm) + ("python-rpy2" ,python-rpy2))) + (home-page "https://github.com/nanoporetech/tombo") + (synopsis "Analysis of raw nanopore sequencing data") + (description "Tombo is a suite of tools primarily for the identification of +modified nucleotides from nanopore sequencing data. Tombo also provides tools +for the analysis and visualization of raw nanopore signal.") + ;; Some parts may be BSD-3-licensed. + (license license:mpl2.0))) + +(define-public python-pyvcf + (package + (name "python-pyvcf") + (version "0.6.8") + ;; Use git, because the PyPI tarballs lack test data. + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jamescasbon/PyVCF.git") + ;; Latest release is not tagged. + (commit "bfcedb9bad1a14074ac4526ffdb610611e073810"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'remove-installed-tests + ;; Do not install test files. + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file-recursively (string-append + (site-packages inputs outputs) + "vcf/test")) + #t))))) + (native-inputs `(("python-cython" ,python-cython))) + (propagated-inputs + `(("python-pysam" ,python-pysam) + ("python-rpy2" ,python-rpy2))) + (home-page "https://github.com/jamescasbon/PyVCF") + (synopsis "Variant Call Format parser for Python") + (description "This package provides a @acronym{VCF,Variant Call Format} +parser for Python.") + (license license:expat))) + +(define-public nanosv + (package + (name "nanosv") + (version "1.2.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "NanoSV" version)) + (sha256 + (base32 + "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) + (build-system python-build-system) + (inputs + `(("python-configparser" ,python-configparser) + ("python-pysam" ,python-pysam) + ("python-pyvcf" ,python-pyvcf))) + (home-page "https://github.com/mroosmalen/nanosv") + (synopsis "Structural variation detection tool for Oxford Nanopore data.") + (description "NanoSV is a software package that can be used to identify +structural genomic variations in long-read sequencing data, such as data +produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION +instruments, or Pacific Biosciences RSII or Sequel sequencers.") + (license license:expat))) + +(define-public r-ascat + (package + (name "r-ascat") + (version "2.5.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Crick-CancerGenomics/ascat.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cc0y3as6cb64iwnx0pgbajiig7m4z723mns9d5i4j09ccid3ccm")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'move-to-ascat-dir + (lambda _ + (chdir "ASCAT")))))) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://github.com/VanLoo-lab/ascat/") + (synopsis "Allele-Specific Copy Number Analysis of Tumors in R") + (description "This package provides the @acronym{ASCAT,Allele-Specific Copy +Number Analysis of Tumors} R package that can be used to infer tumour purity, +ploidy and allele-specific copy number profiles.") + (license license:gpl3))) + +(define-public r-battenberg + (package + (name "r-battenberg") + (version "2.2.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Wedge-lab/battenberg.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-readr" ,r-readr) + ("r-doparallel" ,r-doparallel) + ("r-ggplot2" ,r-ggplot2) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gridextra" ,r-gridextra) + ("r-gtools" ,r-gtools) + ("r-ascat" ,r-ascat))) + (home-page "https://github.com/Wedge-lab/battenberg") + (synopsis "Subclonal copy number estimation in R") + (description "This package contains the Battenberg R package for subclonal +copy number estimation, as described by +@url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}") + (license license:gpl3))) |