Merge branch 'master' into staging

 Conflicts:
	gnu/local.mk
	gnu/packages/gdb.scm
	gnu/packages/lisp-xyz.scm
	gnu/packages/web-browsers.scm

1 files changed, 11 insertions, 10 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d5e6e3d20..e189dd7b00 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -313,7 +313,7 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.9")
+    (version "1.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/samtools/bcftools/"
@@ -321,11 +321,11 @@ BAM files.")
                                   version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
+                "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Delete bundled htslib.
-                          (delete-file-recursively "htslib-1.9")
+                          (delete-file-recursively "htslib-1.11")
                           #t))))
     (build-system gnu-build-system)
     (arguments
@@ -4215,7 +4215,7 @@ performance.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.9")
+    (version "1.11")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4223,7 +4223,7 @@ performance.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
+                "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"))))
     (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
@@ -5613,7 +5613,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.9")
+    (version "1.11")
     (source
      (origin
        (method url-fetch)
@@ -5622,11 +5622,11 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+         "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Delete bundled htslib.
-                   (delete-file-recursively "htslib-1.9")
+                   (delete-file-recursively "htslib-1.11")
                    #t))))
     (build-system gnu-build-system)
     (arguments
@@ -10954,7 +10954,7 @@ programs for inferring phylogenies (evolutionary trees).")
 (define-public imp
   (package
     (name "imp")
-    (version "2.6.2")
+    (version "2.13.0")
     (source
      (origin
        (method url-fetch)
@@ -10962,7 +10962,7 @@ programs for inferring phylogenies (evolutionary trees).")
                            version "/download/imp-" version ".tar.gz"))
        (sha256
         (base32
-         "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
+         "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
     (build-system cmake-build-system)
     (arguments
      `(;; FIXME: Some tests fail because they produce warnings, others fail
@@ -10974,6 +10974,7 @@ programs for inferring phylogenies (evolutionary trees).")
        ("swig" ,swig)
        ("hdf5" ,hdf5)
        ("fftw" ,fftw)
+       ("eigen" ,eigen)
        ("python" ,python-2)))
     (propagated-inputs
      `(("python2-numpy" ,python2-numpy)