gnu: metabat: Update to 2.11.3.

[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 018a262..e372953 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3475,16 +3475,17 @@ form of assemblies or reads.")
 (define-public metabat
   (package
     (name "metabat")
-    (version "2.11.2")
+    (version "2.11.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/berkeleylab/metabat.git")
+             (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
+         "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
        (patches (search-patches "metabat-remove-compilation-date.patch"
                                 "metabat-fix-compilation.patch"))))
     (build-system gnu-build-system)
@@ -4685,6 +4686,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
         'configure
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((out (assoc-ref outputs "out")))
+            ;; Allow 'konfigure.perl' to find 'package.prl'.
+            (setenv "PERL5LIB"
+                    (string-append ".:" (getenv "PERL5LIB")))
+
             ;; The 'configure' script doesn't recognize things like
             ;; '--enable-fast-install'.
             (zero? (system* "./configure"
@@ -8311,6 +8316,30 @@ package, and for letting R applications work on datasets that are larger than
 the available RAM.")
     (license license:artistic2.0)))
 
+(define-public r-annotationfilter
+  (package
+    (name "r-annotationfilter")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationFilter" version))
+              (sha256
+               (base32
+                "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7"))))
+    (properties
+     `((upstream-name . "AnnotationFilter")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-lazyeval" ,r-lazyeval)))
+    (home-page "https://github.com/Bioconductor/AnnotationFilter")
+    (synopsis "Facilities for filtering Bioconductor annotation resources")
+    (description
+     "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources.  The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+    (license license:artistic2.0)))
+
 (define-public emboss
   (package
     (name "emboss")
@@ -8546,25 +8575,24 @@ 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.