;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system go)
#:use-module (guix build-system haskell)
#:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
#:use-module (gnu packages documentation)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages dlang)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
- #:use-module (gnu packages gtk)
+ #:use-module (gnu packages golang)
#:use-module (gnu packages glib)
#:use-module (gnu packages graph)
#:use-module (gnu packages groff)
+ #:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages java)
#:use-module (gnu packages java-compression)
#:use-module (gnu packages jemalloc)
- #:use-module (gnu packages dlang)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.8.0")
+ (version "0.8.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf"))))
+ "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
;; (see: https://github.com/daler/pybedtools/issues/192).
(("def test_getting_example_beds")
"def _do_not_test_getting_example_beds"))
+ ;; This issue still occurs on python2
+ (substitute* "pybedtools/test/test_issues.py"
+ (("def test_issue_303")
+ "def _test_issue_303"))
#t))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system.
(license license:gpl2+)))
(define-public python2-pybedtools
- (package-with-python2 python-pybedtools))
+ (let ((pybedtools (package-with-python2 python-pybedtools)))
+ (package
+ (inherit pybedtools)
+ (native-inputs
+ `(("python2-pathlib" ,python2-pathlib)
+ ,@(package-native-inputs pybedtools))))))
(define-public python-biom-format
(package
(define-public edirect
(package
(name "edirect")
- (version "12.1.20190829")
+ (version "13.3.20200128")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
"/edirect-" version ".tar.gz"))
(sha256
(base32
- "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik"))))
+ "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin (delete-file "Mozilla-CA.tar.gz")
+ (substitute* "rchive.go"
+ ;; This go library does not have any license.
+ (("github.com/fiam/gounidecode/unidecode")
+ "golang.org/rainycape/unidecode"))
+ #t))))
(build-system perl-build-system)
(arguments
`(#:phases
(delete 'configure)
(delete 'build)
(delete 'check) ; simple check after install
+ (add-after 'unpack 'patch-programs
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Ignore errors about missing xtract.Linux and rchive.Linux.
+ (substitute* "pm-refresh"
+ (("cat \\\"\\$target")
+ "grep ^[[:digit:]] \"$target"))
+ #t))
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (install-file "edirect.pl"
- (string-append (assoc-ref outputs "out") "/bin"))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (edirect-go (assoc-ref inputs "edirect-go-programs")))
+ (for-each
+ (lambda (file)
+ (install-file file bin))
+ '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
+ "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
+ "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
+ "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
+ "pm-index" "pm-invert" "pm-merge" "pm-promote"))
+ (symlink (string-append edirect-go "/bin/xtract.Linux")
+ (string-append bin "/xtract"))
+ (symlink (string-append edirect-go "/bin/rchive.Linux")
+ (string-append bin "/rchive")))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
- ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
- (let* ((out (assoc-ref outputs "out"))
+ ;; Make sure everything can run in a pure environment.
+ (let ((out (assoc-ref outputs "out"))
(path (getenv "PERL5LIB")))
- (wrap-program (string-append out "/bin/edirect.pl")
- `("PERL5LIB" ":" prefix (,path))))
- #t))
+ (for-each
+ (lambda (file)
+ (wrap-program file
+ `("PERL5LIB" ":" prefix (,path)))
+ (wrap-program file
+ `("PATH" ":" prefix (,(string-append out "/bin")
+ ,(dirname (which "sed"))
+ ,(dirname (which "gzip"))
+ ,(dirname (which "grep"))
+ ,(dirname (which "perl"))
+ ,(dirname (which "uname"))))))
+ (find-files out ".")))
+ #t))
(add-after 'wrap-program 'check
(lambda* (#:key outputs #:allow-other-keys)
(invoke (string-append (assoc-ref outputs "out")
"-filter" "-help")
#t)))))
(inputs
- `(("perl-html-parser" ,perl-html-parser)
+ `(("edirect-go-programs" ,edirect-go-programs)
+ ("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
("perl-file-listing" ,perl-file-listing)
("perl-html-tagset" ,perl-html-tagset)
extraction of data from document summaries or other results that are returned
in structured XML format. This can eliminate the need for writing custom
software to answer ad hoc questions.")
+ (native-search-paths
+ ;; Ideally this should be set for LWP somewhere.
+ (list (search-path-specification
+ (variable "PERL_LWP_SSL_CA_FILE")
+ (file-type 'regular)
+ (separator #f)
+ (files '("/etc/ssl/certs/ca-certificates.crt")))))
(license license:public-domain)))
+(define-public edirect-go-programs
+ (package
+ (inherit edirect)
+ (name "edirect-go-programs")
+ (build-system go-build-system)
+ (arguments
+ `(#:install-source? #f
+ #:tests? #f ; No tests.
+ #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'build
+ (lambda* (#:key import-path #:allow-other-keys)
+ (with-directory-excursion (string-append "src/" import-path)
+ (invoke "go" "build" "-v" "-x" "j2x.go")
+ (invoke "go" "build" "-v" "-x" "t2x.go")
+ (invoke "go" "build" "-v" "-x" "-o"
+ "xtract.Linux" "xtract.go" "common.go")
+ (invoke "go" "build" "-v" "-x" "-o"
+ "rchive.Linux" "rchive.go" "common.go")
+ (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
+ (replace 'install
+ (lambda* (#:key outputs import-path #:allow-other-keys)
+ (let ((dest (string-append (assoc-ref outputs "out") "/bin"))
+ (source (string-append "src/" import-path "/")))
+ (for-each (lambda (file)
+ (format #t "installing ~a~%" file)
+ (install-file (string-append source file) dest))
+ '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
+ #t))))))
+ (native-inputs '())
+ (propagated-inputs '())
+ (inputs
+ `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
+ ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
+ ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
+ ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
+ ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
+ ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
+ ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
+ ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
+ ("go-golang-org-x-image" ,go-golang-org-x-image)
+ ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+
(define-public exonerate
(package
(name "exonerate")
(define-public star
(package
(name "star")
- (version "2.7.1a")
+ (version "2.7.3a")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alexdobin/STAR.git")
(commit version)))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0n6g4s4hgw7qygs1z97j7a2dgz8gfaa4cv5pjvvvmarvk0x07hyg"))
+ "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq"))
(modules '((guix build utils)))
(snippet
'(begin
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.8.5")
+ (version "0.8.11")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "taxtastic" version))
+ ;; The Pypi version does not include tests.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fhcrc/taxtastic.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
+ "1sv8mkg64jn7zdwf1jj71c16686yrwxk0apb1l8sjszy9p166g0p"))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2
- #:phases
+ `(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-directory
+ (lambda _
+ ;; The git checkout must be writable for tests.
+ (for-each make-file-writable (find-files "."))
+ ;; This test fails, but the error is not caught by the test
+ ;; framework, so the tests fail...
+ (substitute* "tests/test_taxit.py"
+ (("self.cmd_fails\\(''\\)")
+ "self.cmd_fails('nothing')"))
+ ;; This version file is expected to be created with git describe.
+ (mkdir-p "taxtastic/data")
+ (with-output-to-file "taxtastic/data/ver"
+ (lambda () (display ,version)))
+ #t))
+ (add-after 'unpack 'python37-compatibility
+ (lambda _
+ (substitute* "taxtastic/utils.py"
+ (("import csv") "import csv, errno")
+ (("os.errno") "errno"))
+ #t))
(replace 'check
- (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
+ ;; Note, this fails to run with "-v" as it tries to write to a
+ ;; closed output stream.
+ (lambda _ (invoke "python" "-m" "unittest") #t)))))
(propagated-inputs
- `(("python-sqlalchemy" ,python2-sqlalchemy)
- ("python-decorator" ,python2-decorator)
- ("python-biopython" ,python2-biopython)
- ("python-pandas" ,python2-pandas)
- ("python-psycopg2" ,python2-psycopg2)
- ("python-fastalite" ,python2-fastalite)
- ("python-pyyaml" ,python2-pyyaml)
- ("python-six" ,python2-six)
- ("python-jinja2" ,python2-jinja2)
- ("python-dendropy" ,python2-dendropy)))
+ `(("python-sqlalchemy" ,python-sqlalchemy)
+ ("python-decorator" ,python-decorator)
+ ("python-biopython" ,python-biopython)
+ ("python-pandas" ,python-pandas)
+ ("python-psycopg2" ,python-psycopg2)
+ ("python-fastalite" ,python-fastalite)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-six" ,python-six)
+ ("python-jinja2" ,python-jinja2)
+ ("python-dendropy" ,python-dendropy)))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.45-11")
+ (version "1.46-2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90"))))
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
(build-system r-build-system)
(home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/al2na/methylKit")
("r-ggplot2" ,r-ggplot2)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
(home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
(description
(version "1.005")
(source (origin
(method url-fetch)
- (uri (string-append "http://search.maven.org/remotecontent?"
- "filepath=org/biojava/thirdparty/forester/"
+ (uri (string-append "https://repo1.maven.org/maven2/"
+ "org/biojava/thirdparty/forester/"
version "/forester-" version "-sources.jar"))
(file-name (string-append name "-" version ".jar"))
(sha256
(method url-fetch)
(uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
"29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
- "forester/java/classes/resources/synth_look_and_feel_1.xml"))
+ "forester/java/classes/resources/"
+ "synth_look_and_feel_1.xml"))
(file-name (string-append name "-synth-look-and-feel-" version ".xml"))
(sha256
(base32
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "1.1.3")
+ (version "1.1.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi"))))
+ "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9"))))
(build-system gnu-build-system)
(inputs
`(("coreutils" ,coreutils)
(define-public python-pyfaidx
(package
(name "python-pyfaidx")
- (version "0.5.7")
+ (version "0.5.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyfaidx" version))
(sha256
(base32
- "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i"))))
+ "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)))
fasta subsequences.")
(license license:bsd-3)))
+(define-public python2-pyfaidx
+ (package-with-python2 python-pyfaidx))
+
(define-public python-cooler
(package
(name "python-cooler")
(define-public ngless
(package
(name "ngless")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg"))))
+ "1wim8wpqyff080dfcazynrmjwqas38m24m0v350w245mmhrapdma"))))
(build-system haskell-build-system)
(arguments
`(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
(base32
"0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-joblib" ,python-joblib)))
(propagated-inputs
`(("python-click" ,python-click)
("python-cython" ,python-cython)
HCoop / jackhill / guix / guix.git / blobdiff