amaharaneko/guix-mirrors
1
1
Fork 0
mirror of https://codeberg.org/guix/guix.git synced 2025-10-02 02:15:12 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions

Merge branch 'master' into core-updates-frozen

Browse source 
Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/gpodder.scm
	gnu/packages/music.scm
	gnu/packages/patches/glibc-bootstrap-system.patch
	gnu/packages/python-xyz.scm
	gnu/packages/shells.scm
	gnu/packages/statistics.scm
This commit is contained in:
Marius Bakke 2021-07-29 22:34:57 +02:00
commit b029be2ee0
No known key found for this signature in database
GPG key ID: A2A06DF2A33A54FA
100 changed files with 5664 additions and 43929 deletions
Download patch file Download diff file Expand all files Collapse all files

359
gnu/packages/bioinformatics.scm
View file

@ -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)))