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Merge remote-tracking branch 'origin/master' into core-updates-frozen

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Ricardo Wurmus 2021-12-05 19:17:41 +01:00
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gnu/packages/bioinformatics.scm
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@ -830,14 +830,18 @@ provides the Ribotaper pipeline.")
`(#: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")))
#t)))))
prefix "scripts=['scripts/TE.py'],\n"))))))))
(inputs
`(("python-numpy" ,python2-numpy)
("python-matplotlib" ,python2-matplotlib)
@ -1013,7 +1017,7 @@ Python.")
(define-public python-biom-format
(package
(name "python-biom-format")
(version "2.1.7")
(version "2.1.10")
(source
(origin
(method git-fetch)
@ -1025,18 +1029,21 @@ Python.")
(file-name (git-file-name name version))
(sha256
(base32
"1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))
"0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete generated C files.
(for-each delete-file (find-files "." "\\.c"))
#t))))
;; Delete generated C files.
(snippet
'(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1") #t))
(lambda _ (setenv "USE_CYTHON" "1")))
(add-after 'unpack 'relax
(lambda _
(substitute* "setup.py"
(("pytest < 5.3.4") "pytest"))))
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "biom/tests/test_cli/test_validate_table.py"
@ -1048,24 +1055,22 @@ Python.")
(("^(.+)def test_from_hdf5_issue_731" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
#t))
m)))))
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (file) (chmod file #o644))
(find-files out "\\.gz"))
#t))))))
(find-files out "\\.gz"))))))))
(propagated-inputs
`(("python-numpy" ,python-numpy)
`(("python-anndata" ,python-anndata)
("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-flake8" ,python-flake8)
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)
;; FIXME: Upgrade to pandas 1.0 when
;; https://github.com/biocore/biom-format/issues/837 is resolved.
("python-pandas" ,python-pandas-0.25)))
("python-pandas" ,python-pandas)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
@ -1078,23 +1083,7 @@ Python.")
representing counts of observations e.g. operational taxonomic units, KEGG
orthology groups or lipid types, in one or more biological samples
e.g. microbiome samples, genomes, metagenomes.")
(license license:bsd-3)
(properties `((python2-variant . ,(delay python2-biom-format))))))
(define-public python2-biom-format
(let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
(package
(inherit base)
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
`(modify-phases ,phases
;; Do not require the unmaintained pyqi library.
(add-after 'unpack 'remove-pyqi
(lambda _
(substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t)))))))))
(license license:bsd-3)))
(define-public python-pairtools
(package
@ -2690,77 +2679,6 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
(home-page "https://sourceforge.net/projects/codingquarry/")
(license license:gpl3+)))
(define-public couger
(package
(name "couger")
(version "1.8.2")
(source (origin
(method url-fetch)
(uri (string-append
"http://couger.oit.duke.edu/static/assets/COUGER"
version ".zip"))
(sha256
(base32
"04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:phases
(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")))
(copy-recursively "src" (string-append out "/src"))
(mkdir bin)
;; Add "src" directory to module lookup path.
(substitute* "couger"
(("from argparse")
(string-append "import sys\nsys.path.append(\""
out "\")\nfrom argparse")))
(install-file "couger" bin))
#t))
(add-after
'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'couger' runs with the correct PYTHONPATH.
(let* ((out (assoc-ref outputs "out"))
(path (getenv "GUIX_PYTHONPATH")))
(wrap-program (string-append out "/bin/couger")
`("GUIX_PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("python" ,python-2)
("python2-pillow" ,python2-pillow)
("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
("python2-matplotlib" ,python2-matplotlib)))
(propagated-inputs
`(("r-minimal" ,r-minimal)
("libsvm" ,libsvm)
("randomjungle" ,randomjungle)))
(native-inputs
`(("unzip" ,unzip)))
(home-page "http://couger.oit.duke.edu")
(synopsis "Identify co-factors in sets of genomic regions")
(description
"COUGER can be applied to any two sets of genomic regions bound by
paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
putative co-factors that provide specificity to each TF. The framework
determines the genomic targets uniquely-bound by each TF, and identifies a
small set of co-factors that best explain the in vivo binding differences
between the two TFs.
COUGER uses classification algorithms (support vector machines and random
forests) with features that reflect the DNA binding specificities of putative
co-factors. The features are generated either from high-throughput TF-DNA
binding data (from protein binding microarray experiments), or from large
collections of DNA motifs.")
(license license:gpl3+)))
(define-public clustal-omega
(package
(name "clustal-omega")
@ -5070,23 +4988,26 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(("# libraries = z,bz2")
"libraries = z,bz2")
(("include:third-party/zlib:third-party/bzip2")
"include:"))
#t))))
"include:"))))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-cc
(lambda _ (setenv "CC" "gcc") #t))
(lambda _ (setenv "CC" "gcc")))
(add-after 'unpack 'python-3.8-compatibility
(lambda _
;; Python 3.8 removed time.clock().
(substitute* "sandbox/sweep-reads.py"
(("time\\.clock")
"time.process_time"))))
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure .gz files are writable so that the
;; 'reset-gzip-timestamps' phase can do its work.
(let ((out (assoc-ref outputs "out")))
(for-each make-file-writable
(find-files out "\\.gz$"))
#t))))))
(find-files out "\\.gz$"))))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
@ -7764,12 +7685,27 @@ single cell ATAC-seq sequencing data.")
(base32 "0bjzamdw2lcfhlbzc0vdva87c3wwnij8jsvnrpx4wyyxvpcz13m5"))))
(properties `((upstream-name . "umi4cPackage")))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda _
(substitute* "inst/conf/paths.conf"
(("TG3C\\.bowtie2_bin=.*")
(string-append "TG3C.bowtie2_bin="
(which "bowtie2") "\n")))
(substitute* "inst/perl/map3c/TG3C/import3C.pl"
(("\"perl")
(string-append "\"" (which "perl")))))))))
(inputs
`(("perl" ,perl)
("bowtie" ,bowtie)))
(propagated-inputs
`(("r-misha" ,r-misha)
("r-zoo" ,r-zoo)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tanaylab/umi4cpackage")
(synopsis "Processing and analysis of UMI-4C contact profiles.")
(synopsis "Processing and analysis of UMI-4C contact profiles")
(description "This is a package that lets you process UMI-4C data from
scratch to produce nice plots.")
(license license:expat))))
@ -8134,29 +8070,27 @@ Needleman-Wunsch).")
(define-public pardre
(package
(name "pardre")
;; The source of 1.1.5 changed in place, so we append "-1" to the version.
(version "1.1.5-1")
(version "2.2.5")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
"1.1.5" ".tar.gz"))
version ".tar.gz"))
(sha256
(base32
"17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
"105s4f8zs8hh0sc32r9p725n7idza9cj5jvp5z1m5pljjhgk3if5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests included
`(#:tests? #f ; tests require "prove"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "ParDRe" bin)
#t))))))
(install-file "ParDRe" bin)))))))
(inputs
`(("openmpi" ,openmpi)
`(("openmpi-c++" ,openmpi-c++)
("zlib" ,zlib)))
(synopsis "Parallel tool to remove duplicate DNA reads")
(description
@ -9388,7 +9322,7 @@ programs for inferring phylogenies (evolutionary trees).")
(define-public imp
(package
(name "imp")
(version "2.13.0")
(version "2.15.0")
(source
(origin
(method url-fetch)
@ -9396,7 +9330,7 @@ programs for inferring phylogenies (evolutionary trees).")
version "/download/imp-" version ".tar.gz"))
(sha256
(base32
"1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
"05hsrnkpkajppa3f45x4qsarnkj616hlby749zxg4is3bv4i6b5y"))))
(build-system cmake-build-system)
(arguments
`( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used
@ -9409,7 +9343,9 @@ programs for inferring phylogenies (evolutionary trees).")
"IMP.parallel-test_sge.py" ;fail in build container
;; The following test fails non-reproducibly on
;; an inexact numbers assertion.
"IMP.em-medium_test_local_fitting.py")))
"IMP.em-medium_test_local_fitting.py"
;; The following test fails for unknown reasons
"IMP.foxs-add-missing-residues.py")))
(list
(string-append
"-DCMAKE_CTEST_ARGUMENTS="
@ -10321,6 +10257,46 @@ graphs. This library makes it easy to work with @file{.loom} files for
single-cell RNA-seq data.")
(license license:bsd-3)))
(define-public python-biothings-client
(package
(name "python-biothings-client")
(version "0.2.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "biothings_client" version))
(sha256
(base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4"))))
(build-system python-build-system)
(arguments `(#:tests? #false)) ; require internet access
(propagated-inputs `(("python-requests" ,python-requests)))
(home-page "https://github.com/biothings/biothings_client.py")
(synopsis "Python client for BioThings API services")
(description "This package provides a Python client for BioThings
API services.")
(license license:bsd-3)))
(define-public python-mygene
(package
(name "python-mygene")
(version "3.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "mygene" version))
(sha256
(base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7"))))
(build-system python-build-system)
(propagated-inputs
`(("python-biothings-client" ,python-biothings-client)))
(home-page "https://github.com/biothings/mygene.py")
(synopsis "Python Client for MyGene.Info services.")
(description "MyGene.Info provides simple-to-use REST web services
to query/retrieve gene annotation data. It's designed with simplicity
and performance emphasized. Mygene is a Python wrapper to access
MyGene.Info services.")
(license license:bsd-3)))
;; We cannot use the latest commit because it requires Java 9.
(define-public java-forester
(let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
@ -11181,7 +11157,7 @@ based methods.")
(define-public pigx-sars-cov2-ww
(package
(name "pigx-sars-cov2-ww")
(version "0.0.3")
(version "0.0.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
@ -11189,7 +11165,7 @@ based methods.")
"/pigx_sars-cov2-ww-" version ".tar.gz"))
(sha256
(base32
"1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))
"0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs"))
(patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch"))))
(build-system gnu-build-system)
(arguments
@ -11203,9 +11179,13 @@ based methods.")
("autoconf" ,autoconf)))
(inputs
`(("bash-minimal" ,bash-minimal)
("bbmap" ,bbmap)
("bedtools" ,bedtools)
("bwa" ,bwa)
("ensembl-vep" ,ensembl-vep)
("fastp" ,fastp)
("fastqc" ,fastqc)
("ivar" ,ivar)
("kraken2" ,kraken2)
("krona-tools" ,krona-tools)
("lofreq" ,lofreq)
@ -11221,6 +11201,7 @@ based methods.")
("r-minimal" ,r-minimal)
("r-plotly" ,r-plotly)
("r-qpcr" ,r-qpcr)
("r-r-utils" ,r-r-utils)
("r-reshape2" ,r-reshape2)
("r-rmarkdown" ,r-rmarkdown)
("r-stringr" ,r-stringr)
@ -11393,7 +11374,7 @@ version does count multisplits.")
(define-public minimap2
(package
(name "minimap2")
(version "2.18")
(version "2.23")
(source
(origin
(method url-fetch)
@ -11402,7 +11383,7 @@ version does count multisplits.")
"minimap2-" version ".tar.bz2"))
(sha256
(base32
"1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs"))))
"00ngbz1swcgxk5apx9dz5xkh1z8abdpysx5lc7w8fbrfxp41w0j0"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
@ -13824,10 +13805,47 @@ vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots
are generated using @code{ggplot2}.")
(license license:expat)))
(define-public vbz-compression
(package
(name "vbz-compression")
(version "1.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nanoporetech/vbz_compression/")
(commit (string-append "v" version))
;; We include the streamvbyte sources
(recursive? #true)))
(file-name (git-file-name name version))
(sha256
(base32
"1c6wsrnw03vsc5cfp2rdakly5xy55m9chjmy6v685yapdwirdky0"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
'("-DENABLE_CONAN=OFF"
;; Python things aren't even installed, so we might as well
;; disable building them.
"-DENABLE_PYTHON=OFF")))
(inputs
`(;("hdf5" ,hdf5-1.10)
("zstd" ,zstd "lib")))
(native-inputs
`(("googlebenchmark" ,googlebenchmark)))
(home-page "https://github.com/nanoporetech/vbz_compression/")
(synopsis "VBZ compression plugin for nanopore signal data")
(description
"VBZ Compression uses variable byte integer encoding to compress
nanopore signal data. The performance of VBZ is achieved by taking
advantage of the properties of the raw signal and therefore is most
effective when applied to the signal dataset.")
(license license:mpl2.0)))
(define-public python-ont-fast5-api
(package
(name "python-ont-fast5-api")
(version "1.4.4")
(version "4.0.0")
(source
(origin
(method git-fetch)
@ -13837,12 +13855,27 @@ are generated using @code{ggplot2}.")
(file-name (git-file-name name version))
(sha256
(base32
"03cbq4zbbwhll8ml2m9k8sa31mirsvcbjkrq1yna0kkzz9fad5fm"))))
"01hj4751j424lzic2sc4bz1f8w7i7fpkjpy3rgghdyl5lyfyb4s4"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "ont_fast5_api/vbz_plugin"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'copy-plugin
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "ont_fast5_api/vbz_plugin/")
(install-file (string-append
(assoc-ref inputs "vbz-compression")
"/hdf5/lib/plugin/libvbz_hdf_plugin.so")
"ont_fast5_api/vbz_plugin/"))))))
(inputs
`(("vbz-compression" ,vbz-compression)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-six" ,python-six)
("python-h5py" ,python-h5py)
("python-packaging" ,python-packaging)
("python-progressbar33" ,python-progressbar33)))
(home-page "https://github.com/nanoporetech/ont_fast5_api")
(synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format")
@ -14814,6 +14847,7 @@ usually ignored by other methods or only used for filtering.")
(base32
"044xa0hm3b8fga64csrdx05ih8w7kwmvcdrdrhkg8j11ml4bi4xv"))))
(build-system gnu-build-system)
(arguments `(#:parallel-tests? #false)) ; not supported
(inputs
`(("htslib" ,htslib)
("zlib" ,zlib)))