diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 986 |
1 files changed, 670 insertions, 316 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 207f3c3d28..8cdce01e73 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -172,52 +172,54 @@ (define-public aragorn (package (name "aragorn") - (version "1.2.38") + (version "1.2.41") (source (origin (method url-fetch) - (uri (string-append - "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" - version ".tgz")) + (uri (string-append "https://www.ansikte.se/ARAGORN/Downloads/" + "aragorn" version ".c")) (sha256 (base32 - "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) + "0jkzx7sqiarydvz3bwaxh790fpvpkfc926dhsza1dbdhq32ir8wj")))) (build-system gnu-build-system) (arguments - `(#: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" - (string-append "aragorn" ,version ".c")) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (install-file "aragorn" bin) - (install-file "aragorn.1" man)) - #t))))) - (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") + (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:gpl2))) + (license license:gpl3+))) (define-public bamtools (package (name "bamtools") - (version "2.5.1") + (version "2.5.2") (source (origin (method git-fetch) (uri (git-reference @@ -226,21 +228,10 @@ structure of the predicted RNA.") (file-name (git-file-name name version)) (sha256 (base32 - "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b")))) + "14lw571vbks138i0lj66qjdbk8iwa817x2zbpzij61vv1gdgfbn5")))) (build-system cmake-build-system) - (arguments - `(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (add-before - 'configure 'set-ldflags - (lambda* (#:key outputs #:allow-other-keys) - (setenv "LDFLAGS" - (string-append - "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib/bamtools")) - #t))))) - (inputs (list zlib)) + (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 @@ -251,7 +242,7 @@ BAM files.") (define-public bamutils (package (name "bamutils") - (version "1.0.14") + (version "1.0.15") (source (origin (method git-fetch) (uri (git-reference @@ -260,21 +251,22 @@ BAM files.") (file-name (git-file-name name version)) (sha256 (base32 - "0i2r332k1kz0jysyg89d858wqq59n16lw6dv5qmilcwshb77r9v7")))) + "1pxydf9qsr8667jh525bc2wiqn9nwk8rkg05kbyfmjs8d261fl9y")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; Unclear how to run tests - #:make-flags - ,#~(list "USER_WARNINGS=-std=gnu++98" ; - (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")))))) + (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 @@ -287,7 +279,7 @@ BAM files.") (file-name (git-file-name "libstatgen" version)) (sha256 (base32 - "0q9iyk046r4m7qnav8c3f28zsar25lj9nydiklwaswmzdijhi4p1")))))) + "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 @@ -372,7 +364,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.35") + (version "2.4.41") (source (origin (method git-fetch) (uri (git-reference @@ -381,39 +373,49 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (file-name (git-file-name name version)) (sha256 (base32 - "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx")))) + "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l")))) (build-system gnu-build-system) (arguments - '(#:tests? #f - #:make-flags (list (string-append "BINDIR=" %output "/bin")) - #: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")) - #t)) - (delete 'configure)))) + (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=" #$output "/bin"))))))) + (native-inputs + (list diffutils perl which)) (home-page "https://github.com/bedops/bedops") (synopsis "Tools for high-performance genomic feature operations") (description @@ -443,14 +445,15 @@ computational cluster.") "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik")))) (build-system gnu-build-system) (arguments - `(#:test-target "test" - #:make-flags - ,#~(list (string-append "prefix=" #$output)) - #:phases - (modify-phases %standard-phases + (list + #:test-target "test" + #:make-flags + #~(list (string-append "prefix=" #$output)) + #:phases + '(modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (inputs (list samtools zlib)) (home-page "https://github.com/arq5x/bedtools2") @@ -479,63 +482,101 @@ BED, GFF/GTF, VCF.") (base32 "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz")))) (arguments - '(#:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'compatibility - (lambda _ - (substitute* "src/utils/fileType/FileRecordTypeChecker.h" - (("static const float PERCENTAGE") - "static constexpr float PERCENTAGE")) - (substitute* "src/utils/general/DualQueue.h" - (("template <class T, template<class T> class CompareFunc>") - "template <class T, template<class U> class CompareFunc>")))) - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")))))))) + (list + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "src/utils/fileType/FileRecordTypeChecker.h" + (("static const float PERCENTAGE") + "static constexpr float PERCENTAGE")) + (substitute* "src/utils/general/DualQueue.h" + (("template <class T, template<class T> class CompareFunc>") + "template <class T, template<class U> class CompareFunc>")))) + (delete 'configure) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin/"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")))))))) (native-inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (inputs (list samtools zlib)))) (define-public pbcopper - ;; This is the latest commit at the time of this writing. - (let ((commit "ad4143afd25a0bd6adc977c544865c992a515841") + (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-bedtorch + (let ((commit "f5ff4f83b94f59eac660333c64e4b2f296b35cea") (revision "1")) (package - (name "pbcopper") - (version (git-version "1.9.0" revision commit)) + (name "r-bedtorch") + (version (git-version "0.1.12.12" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/pbcopper") + (url "https://github.com/haizi-zh/bedtorch/") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "1qxkbpdkamfisnk36lpi1vdvf3p1lg2hdqna3xgd94pz52bwbmp7")))) - (build-system meson-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-meson-files - (lambda* (#:key inputs #:allow-other-keys) - (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") + "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 pbcopper library provides a suite of data structures, algorithms, -and utilities for PacBio C++ applications.") - (license license:bsd-3)))) + "The goal of bedtorch is to provide a fast BED file manipulation tool +suite native in R.") + (license license:expat)))) (define-public r-btools (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") @@ -573,10 +614,37 @@ and utilities for PacBio C++ applications.") for all types of microbial diversity analyses.") (license license:expat)))) +(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 pbbam (package (name "pbbam") - (version "1.7.0") + (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference @@ -585,7 +653,7 @@ for all types of microbial diversity analyses.") (file-name (git-file-name name version)) (sha256 (base32 - "1avdm5hwhr5ls79017blyalx1npzbf1aa6dgb6j6lg8sq4nk9yyg")))) + "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc")))) (build-system meson-build-system) (arguments `(#:phases @@ -606,13 +674,13 @@ for all types of microbial diversity analyses.") (string-append "'" (which "sh") "'")))))))) ;; These libraries are listed as "Required" in the pkg-config file. (propagated-inputs - (list htslib pbcopper zlib)) + (list htslib-1.14 pbcopper zlib)) (inputs (list boost samtools)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) ; for tests + (list googletest + pkg-config + python-wrapper)) ;for tests (home-page "https://github.com/PacificBiosciences/pbbam") (synopsis "Work with PacBio BAM files") (description @@ -683,8 +751,7 @@ speedup comes during compression.") m (format #f "cpp.find_library('hdf5', dirs : '~a'), \ cpp.find_library('hdf5_cpp', dirs : '~a'), " - hdf5 hdf5))))) - #t)) + 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 @@ -693,8 +760,7 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " (("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")))) - #t))) + (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 @@ -814,26 +880,23 @@ provides the Ribotaper pipeline.") (base32 "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) (build-system gnu-build-system) - (inputs - (list zlib)) - (native-inputs - (list bison)) + (inputs (list zlib)) + (native-inputs (list bison)) (arguments - `(#:tests? #f ; There are no tests to run. - ;; Bison must generate files, before other targets can build. - #:parallel-build? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (man (string-append out "/share/man/man1"))) - (mkdir-p man) - (copy-file "awk.1" (string-append man "/bioawk.1")) - (install-file "bioawk" bin)) - #t))))) + (list + #:tests? #f ; There are no tests to run. + ;; Bison must generate files, before other targets can build. + #:parallel-build? #f + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin")) + (man (string-append #$output "/share/man/man1"))) + (mkdir-p man) + (copy-file "awk.1" (string-append man "/bioawk.1")) + (install-file "bioawk" bin))))))) (home-page "https://github.com/lh3/bioawk") (synopsis "AWK with bioinformatics extensions") (description "Bioawk is an extension to Brian Kernighan's awk, adding the @@ -1237,21 +1300,21 @@ sequencing.") (define-public python-biopython (package (name "python-biopython") - (version "1.76") + (version "1.80") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0wlch9xpa0fpgjzyxi6jsfca6iakaq9a05927xg8vqnmvaccnwrq")))) - (build-system python-build-system) + "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j")))) + (build-system pyproject-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases (add-before 'check 'set-home ;; Some tests require a home directory to be set. - (lambda _ (setenv "HOME" "/tmp") #t))))) + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-numpy)) (home-page "https://biopython.org/") @@ -2077,8 +2140,7 @@ genome (2.9 GB for paired-end).") '(begin ;; Remove bundled SeqAn and samtools (delete-file-recursively "src/SeqAn-1.4.2") - (delete-file-recursively "src/samtools-0.1.18") - #t)))) + (delete-file-recursively "src/samtools-0.1.18"))))) (build-system gnu-build-system) (arguments '(#:parallel-build? #f ; not supported @@ -2093,8 +2155,7 @@ genome (2.9 GB for paired-end).") (string-join (delete (string-append gcc "/include/c++") (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) - ":")) - #t))) + ":"))))) (add-after 'unpack 'use-system-samtools (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makefile.in" @@ -2114,8 +2175,7 @@ genome (2.9 GB for paired-end).") "src/map2gtf.h" "src/align_status.h") (("#include <bam.h>") "#include <samtools/bam.h>") - (("#include <sam.h>") "#include <samtools/sam.h>")) - #t))))) + (("#include <sam.h>") "#include <samtools/sam.h>"))))))) (native-inputs `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions (inputs @@ -2267,23 +2327,34 @@ off-target reads for a capture method that targets CpG-rich region.") (define-public python-bx-python (package (name "python-bx-python") - (version "0.8.12") + (version "0.9.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bxlab/bx-python") - (commit "f4e6a5c93e719db69b5798b6fdd9b167da358316"))) + (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef"))) (file-name (git-file-name name version)) (sha256 (base32 - "0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc")))) - (build-system python-build-system) + "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace"))) + ;; Unrecognized argument. + (add-after 'unpack 'disable-cython-doctests + (lambda _ (substitute* "pytest.ini" (("--doctest-cython") ""))))))) (propagated-inputs (list python-numpy)) (inputs (list zlib)) (native-inputs - (list python-lzo python-nose python-cython)) + (list python-cython python-lzo python-pytest)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -2329,7 +2400,7 @@ has several key features: (define-public python-pysam (package (name "python-pysam") - (version "0.18.0") + (version "0.20.0") (source (origin (method git-fetch) ;; Test data is missing on PyPi. @@ -2339,12 +2410,12 @@ has several key features: (file-name (git-file-name name version)) (sha256 (base32 - "042ca27r6634xg2ixgvq1079cp714wmm6ml7bwc1snn0wxxzywfg")) + "1dq6jwwm98lm30ijdgqc5xz5ppda4nj999y6qs78mhw8x0kij8gg")) (modules '((guix build utils))) (snippet '(begin ;; FIXME: Unbundle samtools and bcftools. (delete-file-recursively "htslib"))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -2413,17 +2484,31 @@ UCSC genome browser.") (define-public python-plastid (package (name "python-plastid") - (version "0.5.1") + (version "0.6.0") (source (origin - (method url-fetch) - (uri (pypi-uri "plastid" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/joshuagryphon/plastid") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1a7mdky2xw02y88l51f58pqk8039ahdp6sblj3zx58zarmy2pqyl")))) - (build-system python-build-system) + "1ka9j08j6i105l89w8b7sg0l8lm3lcrxzy4cjl5dp4cxdmycap62")))) + (build-system pyproject-build-system) (arguments - ;; Some test files are not included. - `(#:tests? #f)) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-test-data + (lambda* (#:key inputs #:allow-other-keys) + (invoke "tar" "-C" "plastid/test" + "-xf" (assoc-ref inputs "test-data")) + ;; This one requires bowtie-build + (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python3" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs (list python-numpy python-scipy @@ -2433,8 +2518,18 @@ UCSC genome browser.") python-biopython python-twobitreader python-termcolor)) + (inputs + (list openssl)) (native-inputs - (list python-cython python-nose)) + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("test-data" + ,(origin + (method url-fetch) + (uri "https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=1") + (file-name "plastid-test-data-2022-05-04.tar.bz2") + (sha256 + (base32 "1szsji06m2r21flnvxg84jnj5zmlk6z10c9651v9ag71nxj9rbzn")))))) (home-page "https://github.com/joshuagryphon/plastid") (synopsis "Python library for genomic analysis") (description @@ -3642,6 +3737,81 @@ software to answer ad hoc questions.") go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-bamnostic + (package + (name "python-bamnostic") + (version "1.1.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "bamnostic" version)) + (sha256 + (base32 + "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pytest)) + (home-page "https://github.com/betteridiot/bamnostic/") + (synopsis "Tool for binary alignment map, random access and parsing") + (description + "Bamnostic is a pure Python @dfn{Binary Alignment Map} (BAM) file parser +and random access tool.") + (license license:bsd-3))) + +(define-public python-episcanpy + (package + (name "python-episcanpy") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "episcanpy" version)) + (sha256 + (base32 + "1qqcyhyzy6idpjmidfdpzwk02hbxm25rymz42h51nlk0vd4r2wwm")))) + (build-system pyproject-build-system) + (arguments + (list + ;; The tests import episcanpy.api, but this is known to not work. + ;; See https://github.com/colomemaria/epiScanpy/issues/133 + #:tests? #false + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs + (list python-anndata + python-bamnostic + python-h5py + python-intervaltree + python-joblib + python-kneed + python-legacy-api-wrap + python-matplotlib + python-natsort + python-networkx + python-numba + python-numpy + python-packaging + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-tqdm + python-pysam + python-tbb + python-umap-learn)) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/colomemaria/epiScanpy") + (synopsis "Tool for epigenomics single cell analysis") + (description + "EpiScanpy is a toolkit to analyse single-cell open +chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018).") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate") @@ -4730,7 +4900,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.14") + (version "1.16") (source (origin (method url-fetch) (uri (string-append @@ -4738,7 +4908,7 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd")))) + "093r1n4s134k50m9a925yn95gyi90ps5dlgc6gq4qwvkzxx7qsv0")))) (build-system gnu-build-system) ;; Let htslib translate "gs://" and "s3://" to regular https links with ;; "--enable-gcs" and "--enable-s3". For these options to work, we also @@ -4764,6 +4934,18 @@ 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-1.14 + (package/inherit htslib + (version "1.14") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd")))))) + (define-public htslib-1.12 (package/inherit htslib (version "1.12") @@ -6945,19 +7127,19 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.8.0") + (version "0.8.4") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) - (build-system python-build-system) + "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0")))) + (build-system pyproject-build-system) (inputs - (list python-biopython)) + (list python-biopython python-pygtrie)) (native-inputs - (list python-nose)) + (list python-pytest)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -10843,25 +11025,12 @@ API services.") (sha256 (base32 "1b4qyngwagh5sc2ygyfqyirg63myzh1g1glk03a1ykxfii32cjlp")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments (list #:tests? #f ;pypi source does not contain tests #:phases #~(modify-phases %standard-phases - (replace 'build - (lambda _ - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'install - (lambda _ - (for-each - (lambda (wheel) - (format #t wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" #$output))) - (find-files "dist" "\\.whl$")))) (add-before 'sanity-check 'set-env (lambda _ ;; numba RuntimeError: cannot cache function 'rdist' @@ -12811,32 +12980,35 @@ implementation differs in these ways: (sha256 (base32 "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$"))))) - ;; Numba needs a writable dir to cache functions. - (add-before 'check 'set-numba-cache-dir - (lambda _ - (setenv "NUMBA_CACHE_DIR" "/tmp"))) - (replace 'check - (lambda* (#:key tests? inputs #:allow-other-keys) - (when tests? + (list + #:test-flags + '(list "-k" + ;; Plot tests that fail. + (string-append "not test_dotplot_matrixplot_stacked_violin" + " and not test_violin_without_raw" + " and not test_correlation" + " and not test_scatterplots" + " and not test_scatter_embedding_add_outline_vmin_vmax_norm" + " and not test_paga" + " and not test_paga_compare" + " and not test_clustermap" + + ;; These try to connect to the network + " and not test_scrublet_plots" + " and not test_plot_rank_genes_groups_gene_symbols" + " and not test_pca_n_pcs" + " and not test_pca_chunked" + " and not test_pca_sparse" + " and not test_pca_reproducible")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'pretend-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (add-after 'unpack 'delete-bad-tests + (lambda _ ;; These tests require Internet access. (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") @@ -12863,27 +13035,11 @@ implementation differs in these ways: (setenv "PYTHONPATH" (string-append (getcwd) ":" - (assoc-ref inputs "python-anndata:source") ":" - (getenv "GUIX_PYTHONPATH"))) - (invoke "pytest" "-vv" - "-k" - ;; Plot tests that fail. - (string-append "not test_dotplot_matrixplot_stacked_violin" - " and not test_violin_without_raw" - " and not test_correlation" - " and not test_scatterplots" - " and not test_scatter_embedding_add_outline_vmin_vmax_norm" - " and not test_paga" - " and not test_paga_compare" - " and not test_clustermap" - - ;; These try to connect to the network - " and not test_scrublet_plots" - " and not test_plot_rank_genes_groups_gene_symbols" - " and not test_pca_n_pcs" - " and not test_pca_chunked" - " and not test_pca_sparse" - " and not test_pca_reproducible")))))))) + #$(this-package-native-input "python-anndata:source") ":" + (getenv "GUIX_PYTHONPATH"))))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (propagated-inputs (list python-anndata python-dask @@ -13373,7 +13529,7 @@ includes operations like compartment, insulation or peak calling.") (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "15") + (version "16") (source (origin ;;Pypi sources do not contain any test @@ -13384,11 +13540,12 @@ includes operations like compartment, insulation or peak calling.") (file-name (git-file-name name version)) (sha256 (base32 - "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) - (build-system python-build-system) + "00b9l62j4knrsdp7l3pawi9cqcsl09diycbhmmnar850bzssmq4f")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -13412,7 +13569,7 @@ the HiCExplorer and pyGenomeTracks packages.") (define-public python-hicexplorer (package (name "python-hicexplorer") - (version "2.1.4") + (version "3.7.2") (source (origin ;; The latest version is not available on Pypi. @@ -13423,32 +13580,114 @@ the HiCExplorer and pyGenomeTracks packages.") (file-name (git-file-name name version)) (sha256 (base32 - "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) - (build-system python-build-system) + "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-up-requirements - (lambda _ - (substitute* "setup.py" - (("==") ">=")) - #t))))) + (list + #:test-flags + '(list "hicexplorer/test/general/" + "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py" + "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py" + "-k" + (string-append + ;; Unknown chromosome: ChrX + "not test_build_matrix_restrictionCutFile_two" + ;; fixture 'keepSelfLigation' not found + " and not test_build_matrix_restrictionCutFile_six" + ;; ValueError: object dtype is not supported by sparse matrices + " and not test_hic_transfer_obs_exp_perChromosome" + + ;; No KR balancing available + " and not test_correct_matrix_KR_partial_cool" + " and not test_correct_matrix_KR_cool" + " and not test_correct_matrix_KR_H5")) + #:phases + #~(modify-phases %standard-phases + ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23 + (add-after 'unpack 'remove-dependency-on-krbalancing + (lambda _ + (substitute* "hicexplorer/hicCorrectMatrix.py" + (("from krbalancing import.*") "") + (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent) + (string-append m "\n" + indent "log.error('krbalancing not available')\n" + indent "exit(1)"))) + (substitute* "setup.py" + (("\"krbalancing >= 0.0.5\",") "")) + (substitute* "requirements.txt" + (("krbalancing >= 0.0.5") "")))) + (add-after 'unpack 'fix-references + (lambda _ + (let ((site (string-append #$output "/lib/python" + #$(version-major+minor + (package-version python)) + "/site-packages"))) + (substitute* "hicexplorer/lib/tadClassifier.py" + (("model_location = site.getsitepackages\\(\\)\\[0\\]") + (string-append "model_location = \"" site "\"")))) + (substitute* "hicexplorer/hicFindRestSite.py" + (("subprocess.check_output\\(\\[\"cat\"") + (string-append "subprocess.check_output([\"" + (which "cat") "\"")) + (("cmd = 'sort -k1") + (string-append "cmd = '" (which "sort") " -k1"))))) + ;; The tests aim to detect available memory and run more tests when + ;; there is more available memory. Let's run them deterministically + ;; instead and don't run any tests that require more than 1GB of + ;; RAM. + (add-after 'unpack 'run-only-low-mem-tests + (lambda _ + (with-directory-excursion "hicexplorer/test" + (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py" + "trivial_runs/test_hicBuildMatrix_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py" + "general/test_hicDifferentialTAD.py" + "general/test_hicDetectLoops.py" + "general/test_hicPlotMatrix.py" + "general/test_hicHyperoptDetectLoops.py" + "general/test_hicCreateThresholdFile.py" + "general/test_hicMergeDomains.py" + "general/test_hicHyperoptDetectLoopsHiCCUPS.py" + "general/test_hicAggregateContacts.py" + "general/test_hicInterIntraTAD.py") + (("^memory =.*") "memory = 1\n")))))))) (propagated-inputs (list python-biopython - python-configparser + python-cleanlab-1 python-cooler + python-fit-nbinom python-future + python-graphviz + python-hic2cool + python-hicmatrix + python-hyperopt + python-imbalanced-learn python-intervaltree + python-ipykernel python-jinja2 python-matplotlib python-numpy python-pandas + python-psutil + python-pybedtools python-pybigwig + python-pygenometracks python-pysam + python-scikit-learn python-scipy - python-six python-tables + python-tqdm python-unidecode)) + (native-inputs + (list graphviz)) ;for hicexplorer/test/test_compute_function.py (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description @@ -13465,25 +13704,25 @@ genomic scores), long range contacts and the visualization of viewpoints.") (define-public python-pygenometracks (package (name "python-pygenometracks") - (version "3.3") + (version "3.5") (source (origin (method url-fetch) (uri (pypi-uri "pyGenomeTracks" version)) (sha256 (base32 - "16laa0wnf4qn9fb9ych4w1vqhqwjss70v0y0f6wp4gwqfrlgac0f")))) - (build-system python-build-system) + "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p")))) + (build-system pyproject-build-system) (arguments - `(#:tests? #f ; there are none - #:phases - (modify-phases %standard-phases + (list + #:tests? #f ;there are none + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" (("matplotlib ==3.1.1") - "matplotlib >=3.1.1")) - #t))))) + "matplotlib >=3.1.1"))))))) (propagated-inputs (list python-future python-gffutils @@ -14142,7 +14381,7 @@ polymorphisms) and indels with respect to a reference genome and more.") (define-public cnvkit (package (name "cnvkit") - (version "0.9.5") + (version "0.9.9") (source (origin (method git-fetch) @@ -14151,17 +14390,28 @@ polymorphisms) and indels with respect to a reference genome and more.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) - (build-system python-build-system) + (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "setup.py" + (("'joblib.*") ""))))))) (propagated-inputs (list python-biopython python-future python-matplotlib python-numpy - python-reportlab python-pandas - python-pysam + python-pomegranate python-pyfaidx + python-pysam + python-reportlab + python-scikit-learn python-scipy ;; R packages r-dnacopy)) @@ -14335,6 +14585,44 @@ contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.") (license license:gpl2+))) +(define-public vembrane + (package + (name "vembrane") + (version "0.13.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vembrane/vembrane") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gdih56gpqd8ks3sd4ah844kac09hi3g073k9gvazb32ah50900w")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("pysam = \"\\^0.19\"") "pysam = \"^0.20\"") + (("numpy = \\{ version = \"\\^1.23\"") + "numpy = { version = \"^1\""))))))) + (inputs + (list python-asttokens python-intervaltree python-numpy + python-pysam python-pyyaml)) + (native-inputs + (list poetry python-pytest)) + (home-page "https://github.com/vembrane/vembrane") + (synopsis "Filter VCF/BCF files with Python expressions.") + (description "Vembrane allows to simultaneously filter variants based on +any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the +annotation field ANN. When filtering based on ANN, annotation entries are +filtered first. If no annotation entry remains, the entire variant is +deleted.") + (license license:expat))) + (define-public python-velocyto (package (name "python-velocyto") @@ -15998,7 +16286,7 @@ coordinates between different assemblies.") (define-public python-cgatcore (package (name "python-cgatcore") - (version "0.6.7") + (version "0.6.14") ;; The version of pypi does not include test data. (source (origin (method git-fetch) @@ -16008,11 +16296,22 @@ coordinates between different assemblies.") (file-name (git-file-name name version)) (sha256 (base32 - "17vk88v1bx7x02ibzkc9i7ir4b5p1hcjr38jpsfzyzxr68352d5k")))) - (build-system python-build-system) + "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:test-flags + '(list "-k" + (string-append + ;; This test actually does what it should, but the check fails with + ;; TypeError: cannot unpack non-iterable Namespace object + "not test_start_and_stop_are_logged_with_argparse" + ;; These all attempt to connect to localhost with SSH + " and not test_job_should_use_TMPDIR_and_clean_up" + " and not test_job_should_use_TMPDIR_and_clean_up_after_fail" + " and not test_job_should_write_to_explicit_temp_and_not_clean_up")) + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ (substitute* "cgatcore/pipeline/execution.py" @@ -16020,21 +16319,22 @@ coordinates between different assemblies.") (("executable=\"/bin/bash\"") (string-append "executable=\"" (which "bash") "\"")) (("\\\\time") (which "time"))))) - (delete 'check) - (add-after 'install 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - ;; Requires network access - (delete-file "tests/test_pipeline_execution.py") - (invoke "python" "-m" "pytest" "-v"))))))) + (add-after 'unpack 'sqlite-compatibility + (lambda _ + ;; Load apsw (and thus newer sqlite3) before importing Python's + ;; older sqlite3 library. + (substitute* "cgatcore/pipeline/__init__.py" + (("import os") + (string-append "import os\nimport apsw"))) + (substitute* "tests/template_pipeline.py" + (("import sys" m) + (string-append "import apsw\n" m)))))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("lsof" ,lsof) - ("hostname" ,inetutils) - ("openssl" ,openssl))) - (inputs - (list time)) + (list python-pytest + lsof + inetutils + openssl)) + (inputs (list time)) (propagated-inputs (list python-apsw python-gevent @@ -16514,18 +16814,31 @@ feature is fast retrieval of range queries into numpy arrays.") (define-public python-dna-features-viewer (package (name "python-dna-features-viewer") - (version "3.0.3") + (version "3.1.1") (source (origin (method url-fetch) (uri (pypi-uri "dna_features_viewer" version)) (sha256 (base32 - "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc")))) - (build-system python-build-system) - (arguments '(#:tests? #false)) ; there are none + "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73 + ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74 + (add-after 'unpack 'fix-biopython-compatibility + (lambda _ + (substitute* "dna_features_viewer/biotools.py" + (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)") + "zip(aa1 + ('*',), aa3 + ('*',))"))))))) (propagated-inputs - (list python-biopython python-matplotlib)) + (list python-biopython + python-matplotlib + python-packaging)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") @@ -17391,6 +17704,47 @@ module capable of computing base-level alignments for very large sequences.") (home-page "https://github.com/ekg/wfmash") (license license:expat))) +(define-public wiggletools + (package + (name "wiggletools") + (version "1.2.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Ensembl/WiggleTools/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1g3qla4l1g583nzlgyww5jqxpq87ndpn9cmjls098bgqjyn5292q")))) + (build-system gnu-build-system) + (arguments + (list + ;; Tests require internet access + #:tests? #false + #:make-flags + #~(list "Wiggletools" + (string-append "CC=" #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "bin/wiggletools" + (string-append #$output "/bin"))))))) + (inputs + (list curl ; XXX: needed by libbigwig + htslib libbigwig gsl xz zlib)) + (home-page "https://github.com/Ensembl/WiggleTools/") + (synopsis "Operations on the space of numerical functions defined on the genome") + (description "The WiggleTools package allows genomewide data files to be +manipulated as numerical functions, equipped with all the standard functional +analysis operators (sum, product, product by a scalar, comparators), and +derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank +sum test, etc).") + (license license:asl2.0))) + (define-public flair (package (name "flair") |