diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 106 |
1 files changed, 70 insertions, 36 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5157046ab..5e98aea91f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3450,7 +3450,7 @@ sequences).") (("^#include \"kseq\\.h\"") "#include \"htslib/kseq.h\"")) #t)) - (add-before 'configure 'autoconf + (add-after 'fix-includes 'autoconf (lambda _ (zero? (system* "autoconf"))))))) (native-inputs `(("autoconf" ,autoconf) @@ -3475,7 +3475,7 @@ form of assemblies or reads.") (define-public metabat (package (name "metabat") - (version "2.11.2") + (version "2.12.1") (source (origin (method url-fetch) @@ -3484,10 +3484,8 @@ form of assemblies or reads.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv")) - (patches (search-patches "metabat-remove-compilation-date.patch" - "metabat-fix-compilation.patch" - "metabat-fix-boost-issue.patch")))) + "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) + (patches (search-patches "metabat-fix-compilation.patch")))) (build-system gnu-build-system) (arguments `(#:phases @@ -4065,7 +4063,7 @@ predicts the locations of structural units in the sequences.") (define-public proteinortho (package (name "proteinortho") - (version "5.16") + (version "5.16b") (source (origin (method url-fetch) @@ -4075,7 +4073,7 @@ predicts the locations of structural units in the sequences.") version "_src.tar.gz")) (sha256 (base32 - "0z4f5cg0cs8ai62hfvp4q6w66q2phcc55nhs4xj5cyhxxivjv2ai")))) + "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -4751,6 +4749,13 @@ simultaneously.") #:tests? #f ; no "check" target #:phases (modify-phases %standard-phases + (add-before 'configure 'set-perl-search-path + (lambda _ + ;; Work around "dotless @INC" build failure. + (setenv "PERL5LIB" + (string-append (getcwd) "/setup:" + (getenv "PERL5LIB"))) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -5056,6 +5061,13 @@ sequence itself can be retrieved from these databases.") "/lib32"))) #:phases (modify-phases %standard-phases + (add-before 'configure 'set-perl-search-path + (lambda _ + ;; Work around "dotless @INC" build failure. + (setenv "PERL5LIB" + (string-append (getcwd) "/setup:" + (getenv "PERL5LIB"))) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) ;; The build system expects a directory containing the sources and @@ -5396,7 +5408,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") #t)) (delete 'configure)))) (native-inputs - `(("vim" ,vim))) ; for xxd + `(("xxd" ,xxd))) (inputs `(("htslib" ,htslib) ("zlib" ,zlib))) @@ -5654,18 +5666,17 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-3") + (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5")))) + "1n57dzv2aid6iqd9fkqik401sidqanhzsawyak94qbiyh6dbd1x9")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-lattice" ,r-lattice) @@ -6126,10 +6137,33 @@ data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) +(define-public r-sparql + (package + (name "r-sparql") + (version "1.16") + (source (origin + (method url-fetch) + (uri (cran-uri "SPARQL" version)) + (sha256 + (base32 + "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) + (properties `((upstream-name . "SPARQL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/SPARQL") + (synopsis "SPARQL client for R") + (description "This package provides an interface to use SPARQL to pose +SELECT or UPDATE queries to an end-point.") + ;; The only license indication is found in the DESCRIPTION file, + ;; which states GPL-3. So we cannot assume GPLv3+. + (license license:gpl3))) + (define-public vsearch (package (name "vsearch") - (version "2.4.3") + (version "2.4.4") (source (origin (method url-fetch) @@ -6139,7 +6173,7 @@ track. The database is exposed as a @code{TxDb} object.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp")) + "1d8a4gjwaqdv57krlr80x18mg5py1bbdiqs5m0jdn38filc9z40k")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -6153,8 +6187,8 @@ track. The database is exposed as a @code{TxDb} object.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'configure 'autogen - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (add-after 'unpack 'autogen + (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) @@ -6433,13 +6467,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.4") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv")))) + "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -7109,13 +7143,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) + "03ysxi9fdd3bcfj05iaysya9knn2aa2irwpypb5srg0xwv92bdb9")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7990,7 +8024,7 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.1.1") + (version "1.3.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" @@ -7998,7 +8032,7 @@ paired-end data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw")))) + "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr) @@ -8019,6 +8053,7 @@ paired-end data.") ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) ("r-topgo" ,r-topgo) ("r-dt" ,r-dt) + ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) ("r-plotrix" ,r-plotrix) ("r-motifrg" ,r-motifrg) @@ -8032,7 +8067,7 @@ paired-end data.") intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.") (home-page "https://github.com/BIMSBbioinfo/RCAS") - (license license:expat))) + (license license:artistic2.0))) (define-public rcas-web (package @@ -8370,14 +8405,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) AM_CONDITIONAL(AMPNG, true)")) #t)) - (add-after 'unpack 'disable-update-check + (add-after 'fix-checks 'disable-update-check (lambda _ ;; At build time there is no connection to the Internet, so ;; looking for updates will not work. (substitute* "Makefile.am" (("\\$\\(bindir\\)/embossupdate") "")) #t)) - (add-before 'configure 'autogen + (add-after 'disable-update-check 'autogen (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs `(("perl" ,perl) @@ -8575,25 +8610,24 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "0.9") + (version "1.2") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny")) - (patches (search-patches "multiqc-fix-git-subprocess-error.patch")))) + "032svgym67k2ds7wp0cxzv79gi30yrdl45zbqn74lni3dk04qm33")))) (build-system python-build-system) - (arguments - ;; Tests are to be introduced in the next version, see - ;; https://github.com/ewels/MultiQC/issues/376 - `(#:tests? #f)) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) ("python-click" ,python-click) + ("python-spectra" ,python-spectra) + ("python-requests" ,python-requests) + ("python-markdown" ,python-markdown) + ("python-lzstring" ,python-lzstring) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) ;; MultQC checks for the presence of nose at runtime. @@ -8830,14 +8864,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.16.2") + (version "1.16.4") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr")))) + "1pmhsfvd45a44xdiml4zx3zd5fhygqyziqvygahkk9yibnyhv4cv")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/MALDIquant") @@ -9443,7 +9477,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (substitute-keyword-arguments (package-arguments htslib) ((#:phases phases) `(modify-phases ,phases - (add-before 'configure 'bootstrap + (add-after 'unpack 'bootstrap (lambda _ (zero? (system* "autoreconf" "-vif")))))))) (native-inputs |