diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 37 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5157046ab..1f1b686c71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 @@ -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 @@ -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) @@ -6129,7 +6140,7 @@ track. The database is exposed as a @code{TxDb} object.") (define-public vsearch (package (name "vsearch") - (version "2.4.3") + (version "2.4.4") (source (origin (method url-fetch) @@ -6139,7 +6150,7 @@ 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 @@ -6433,13 +6444,13 @@ 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 +7120,13 @@ 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 +8001,7 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.1.1") + (version "1.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" @@ -7998,7 +8009,7 @@ paired-end data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw")))) + "19mk7vkbngmch54kzcxb52161ljfchhjsaanza8iwv5h98sjj66d")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr) @@ -8032,7 +8043,7 @@ 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 @@ -8575,25 +8586,24 @@ 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 +8840,14 @@ 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") |