branch master updated (30f0d21 -> 03592a6)

[Maxim Cournoyer]

apteryx pushed a change to branch master
in repository guix.

  from  30f0d21   gnu: Add nanopolish.
   new  03592a6   gnu: emacs-realgud: Patch configure.ac to repair the 
build.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk   |  2 ++
 gnu/packages/emacs.scm |  6 -
 .../patches/emacs-realgud-fix-configure-ac.patch   | 27 ++
 3 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/emacs-realgud-fix-configure-ac.patch

01/01: gnu: emacs-realgud: Patch configure.ac to repair the build.

[Maxim Cournoyer]

apteryx pushed a commit to branch master
in repository guix.

commit 03592a6f882f5b4309f77c3dc3e65559d7b7cb75
Author: Maxim Cournoyer 
Date:   Wed Oct 31 00:24:04 2018 -0400

gnu: emacs-realgud: Patch configure.ac to repair the build.

This fixes https://bugs.gnu.org/33196, a build problem caused by a defective
Elisp snippet in a check in configure.ac.

* gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs.scm (emacs-realgud)[source]: Use it.
---
 gnu/local.mk   |  2 ++
 gnu/packages/emacs.scm |  6 -
 .../patches/emacs-realgud-fix-configure-ac.patch   | 27 ++
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 23a6cb3..2a90a85 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -19,6 +19,7 @@
 # Copyright © 2018 Amirouche Boubekki 
 # Copyright © 2018 Oleg Pykhalov 
 # Copyright © 2018 Stefan Stefanović 
+# Copyright © 2018 Maxim Cournoyer 
 #
 # This file is part of GNU Guix.
 #
@@ -663,6 +664,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch   \
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch\
   %D%/packages/patches/emacs-source-date-epoch.patch   \
+  %D%/packages/patches/emacs-realgud-fix-configure-ac.patch\
   %D%/packages/patches/enlightenment-fix-setuid-path.patch \
   %D%/packages/patches/erlang-man-path.patch   \
   %D%/packages/patches/eudev-rules-directory.patch \
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 3e32998..ce1add3 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3659,7 +3659,11 @@ after buffer changes.")
version ".tar"))
(sha256
 (base32
- "108wgxg7fb4byaiasgvbxv2hq7b00biq9f0mh9hy6vw4160y5w24"
+ "108wgxg7fb4byaiasgvbxv2hq7b00biq9f0mh9hy6vw4160y5w24"))
+   (patches
+;; Patch awaiting inclusion upstream (see:
+;; https://github.com/realgud/realgud/pull/226).
+(search-patches "emacs-realgud-fix-configure-ac.patch"
 (build-system emacs-build-system)
 (arguments
  `(#:tests? #t
diff --git a/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch 
b/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch
new file mode 100644
index 000..8165857
--- /dev/null
+++ b/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch
@@ -0,0 +1,27 @@
+From a293690f29407ac54a218d6d20c2142e1a0319d1 Mon Sep 17 00:00:00 2001
+From: Maxim Cournoyer 
+Date: Wed, 31 Oct 2018 00:08:34 -0400
+Subject: [PATCH] configure.ac: Fix NO_CHECK_EMACS_PACKAGES elisp.
+
+Remove the extraneous trailing parenthesis.
+---
+ configure.ac | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index de0d932..69bcea7 100644
+--- a/configure.ac
 b/configure.ac
+@@ -25,8 +25,7 @@ AC_MSG_NOTICE("Checking prerequiste packages")
+ $EMACS -batch -q --no-site-file -eval \
+   '(dolist (package
+  (quote (cl-lib loc-changes load-relative test-simple)))
+-(require package))
+-   )'
++(require package))'
+ fi
+ if test $? -ne 0 ; then
+ AC_MSG_ERROR([Can't continue until above error is corrected.])
+-- 
+2.19.0
+

branch master updated (c61f36f -> 30f0d21)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  c61f36f   doc: Fix typo in connman config.
   new  30f0d21   gnu: Add nanopolish.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm | 74 +
 1 file changed, 74 insertions(+)

01/01: gnu: Add nanopolish.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 30f0d21b407756e88cd960a9678b6af0a1ad80e9
Author: pimi 
Date:   Mon Nov 12 21:59:49 2018 +0100

gnu: Add nanopolish.

* gnu/packages/bioinformatics.scm (nanopolish): New variable.

Signed-off-by: Ricardo Wurmus 
---
 gnu/packages/bioinformatics.scm | 74 +
 1 file changed, 74 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1a71992..dc36ced 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14362,3 +14362,77 @@ both read length (longer is better) and read identity 
(higher is better) when
 choosing which reads pass the filter.")
   (license (list license:gpl3   ;filtlong
  license:asl2.0) ;histogram.py
+
+(define-public nanopolish
+  ;; The recommended way to install is to clone the git repository
+  ;; .
+  ;; Also, the differences between release and current version seem to be
+  ;; significant.
+  (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d")
+(revision "1"))
+(package
+  (name "nanopolish")
+  (version (git-version "0.10.2" revision commit))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/jts/nanopolish.git;)
+   (commit commit)
+   (recursive? #t)))
+ (file-name (git-file-name name version))
+ (sha256
+  (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6"
+  (build-system gnu-build-system)
+  (arguments
+   `(#:make-flags
+ `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
+ #:tests? #f; no check target
+ #:phases
+ (modify-phases %standard-phases
+   (add-after 'unpack 'find-eigen
+ (lambda* (#:key inputs #:allow-other-keys)
+   (setenv "CPATH"
+   (string-append (assoc-ref inputs "eigen")
+  "/include/eigen3"))
+   #t))
+   (delete 'configure)
+   (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+   (let* ((out (assoc-ref outputs "out"))
+  (bin (string-append out "/bin"))
+  (scripts (string-append out 
"/share/nanopolish/scripts")))
+
+ (install-file "nanopolish" bin)
+ (for-each (lambda (file) (install-file file scripts))
+   (find-files "scripts" ".*"))
+ #t)))
+   (add-after 'install 'wrap-programs
+ (lambda* (#:key outputs #:allow-other-keys)
+   (for-each (lambda (file)
+   (wrap-program file `("PYTHONPATH" ":" prefix 
(,path
+ (find-files "/share/nanopolish/scripts" "\\.py"))
+   (for-each (lambda (file)
+   (wrap-program file `("PERL5LIB" ":" prefix 
(,path
+ (find-files  "/share/nanopolish/scripts" "\\.pl"))
+   #t)
+  (inputs
+   `(("eigen" ,eigen)
+ ("hdf5" ,hdf5)
+ ("htslib" ,htslib)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("python-biopython" ,python-biopython)
+ ("python-numpy" ,python-numpy)
+ ("python-pysam" ,python-pysam)
+ ("python-scikit-learn" , python-scikit-learn)
+ ("python-scipy" ,python-scipy)
+ ("zlib" ,zlib)))
+  (home-page "https://github.com/jts/nanopolish;)
+  (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
+  (description
+   "This package analyses the Oxford Nanopore sequencing data at 
signal-level.
+Nanopolish can calculate an improved consensus sequence for a draft genome
+assembly, detect base modifications, call SNPs (Single nucleotide
+polymorphisms) and indels with respect to a reference genome and more.")
+  (license license:expat

branch master updated (2d86eaf -> c61f36f)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  2d86eaf   gnu: sambamba: Update to 0.6.8.
   new  c61f36f   doc: Fix typo in connman config.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

01/01: doc: Fix typo in connman config.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit c61f36f368c563c48815de0abe625383909b0a8d
Author: Giovanni Biscuolo 
Date:   Wed Nov 14 21:44:13 2018 +0100

doc: Fix typo in connman config.

* doc/guix.texi (Networking Services): Fix typo in connman config
"disable-vpn?" parameter documentation, semantic is inverted.

Signed-off-by: Efraim Flashner 
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 0ba034e..765261f 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11832,7 +11832,7 @@ Data Type representing the configuration of connman.
 The connman package to use.
 
 @item @code{disable-vpn?} (default: @code{#f})
-When true, enable connman's vpn plugin.
+When true, disable connman's vpn plugin.
 @end table
 @end deftp
 

branch master updated (7413c31 -> 2d86eaf)

[Roel Janssen]

roelj pushed a change to branch master
in repository guix.

  from  7413c31   gnu: linux-libre: Update to 4.19.2.
   new  2d86eaf   gnu: sambamba: Update to 0.6.8.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm | 25 +
 1 file changed, 13 insertions(+), 12 deletions(-)

01/01: gnu: sambamba: Update to 0.6.8.

[Roel Janssen]

roelj pushed a commit to branch master
in repository guix.

commit 2d86eaff5bb8ca8c8ca74b47a6a7d964ec7c8b22
Author: Roel Janssen 
Date:   Thu Nov 15 13:09:01 2018 +0100

gnu: sambamba: Update to 0.6.8.

* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
---
 gnu/packages/bioinformatics.scm | 25 +
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 58cee5c..1a71992 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11158,7 +11158,7 @@ droplet sequencing.  It has been particularly tailored 
for Drop-seq.")
 (define-public sambamba
   (package
 (name "sambamba")
-(version "0.6.7-10-g223fa20")
+(version "0.6.8")
 (source
  (origin
(method git-fetch)
@@ -11168,7 +11168,7 @@ droplet sequencing.  It has been particularly tailored 
for Drop-seq.")
(file-name (string-append name "-" version "-checkout"))
(sha256
 (base32
- "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"
+ "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"
 (build-system gnu-build-system)
 (arguments
  `(#:tests? #f  ; there is no test target
@@ -11179,9 +11179,10 @@ droplet sequencing.  It has been particularly tailored 
for Drop-seq.")
  (add-after 'unpack 'fix-ldc-version
(lambda _
  (substitute* "gen_ldc_version_info.py"
-   (("/usr/bin/env.*") (which "python")))
+   (("/usr/bin/env.*") (which "python3")))
  (substitute* "Makefile"
-   (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
+   ;; We use ldc2 instead of ldmd2 to compile sambamba.
+   (("\\$\\(shell which ldmd2\\)") (which "ldc2")))
  #t))
  (add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
@@ -11193,21 +11194,21 @@ droplet sequencing.  It has been particularly 
tailored for Drop-seq.")
  (substitute* "Makefile"
(("htslib/libhts.a lz4/lib/liblz4.a")
 "-L-lhts -L-llz4")
-   ((" htslib-static lz4-static") ""))
+   ((" lz4-static htslib-static") ""))
  #t))
  (replace 'install
(lambda* (#:key outputs #:allow-other-keys)
  (let* ((out   (assoc-ref outputs "out"))
 (bin   (string-append out "/bin")))
(mkdir-p bin)
-   (install-file "build/sambamba" bin)
+   (install-file "bin/sambamba" bin)
#t))
 (native-inputs
  `(("ldc" ,ldc)
("rdmd" ,rdmd)
-   ("python" ,python2-minimal)
+   ("python" ,python-minimal)
("biod"
-,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
+,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
(origin
  (method git-fetch)
  (uri (git-reference
@@ -11218,20 +11219,20 @@ droplet sequencing.  It has been particularly 
tailored for Drop-seq.")
"-checkout"))
  (sha256
   (base32
-   "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")
+   "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")
("undead"
-,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
+,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
(origin
  (method git-fetch)
  (uri (git-reference
-   (url "https://github.com/dlang/undeaD.git;)
+   (url "https://github.com/biod/undeaD.git;)
(commit commit)))
  (file-name (string-append "undead-"
(string-take commit 9)
"-checkout"))
  (sha256
   (base32
-   "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))
+   "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))
 (inputs
  `(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))