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7d958f00d01dc6'>e2cdc9b0938e5ed7ac1b095b83c5760bbedecb87 /gnu parent3f7ae420d8a54d4e2ab7f349c40d8930fe9e0771 (diff)parent040d35f088e0f1c856f3f5a9b6bf889b17bd68b3 (diff)downloadguix-d1252b597d8b6c77746da7b7417d958f00d01dc6.tar.gz
guix-d1252b597d8b6c77746da7b7417d958f00d01dc6.zip
Merge remote-tracking branch 'origin/master' into core-updates
Diffstat (limited to 'gnu')
-rw-r--r--gnu/home/services/ssh.scm65
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm331
-rw-r--r--gnu/packages/emacs-xyz.scm57
-rw-r--r--gnu/packages/engineering.scm14
-rw-r--r--gnu/packages/games.scm51
-rw-r--r--gnu/packages/gnome.scm8
-rw-r--r--gnu/packages/guile-xyz.scm6
-rw-r--r--gnu/packages/linux.scm30
-rw-r--r--gnu/packages/lxqt.scm10
-rw-r--r--gnu/packages/mpd.scm4
-rw-r--r--gnu/packages/networking.scm4
-rw-r--r--gnu/packages/parallel.scm29
-rw-r--r--gnu/packages/patches/clog-fix-shared-build.patch85
-rw-r--r--gnu/packages/pretty-print.scm4
-rw-r--r--gnu/packages/python-crypto.scm1
-rw-r--r--gnu/packages/text-editors.scm5
-rw-r--r--gnu/packages/web-browsers.scm94
-rw-r--r--gnu/packages/wm.scm8
-rw-r--r--gnu/services/base.scm134
-rw-r--r--gnu/services/databases.scm14
-rw-r--r--gnu/services/dns.scm1
-rw-r--r--gnu/services/herd.scm12
-rw-r--r--gnu/services/rsync.scm8
-rw-r--r--gnu/tests.scm112
-rw-r--r--gnu/tests/base.scm2
-rw-r--r--gnu/tests/install.scm4
27 files changed, 720 insertions, 374 deletions
diff --git a/gnu/home/services/ssh.scm b/gnu/home/services/ssh.scm
index 01917a29cd..6aeb6ad5a7 100644
--- a/gnu/home/services/ssh.scm
+++ b/gnu/home/services/ssh.scm
@@ -20,6 +20,7 @@
(define-module (gnu home services ssh)
#:use-module (guix gexp)
#:use-module (guix records)
+ #:use-module (guix deprecation)
#:use-module (guix diagnostics)
#:use-module (guix i18n)
#:use-module (gnu services)
@@ -32,6 +33,8 @@
#:autoload (gnu packages base) (glibc-utf8-locales)
#:use-module (gnu packages ssh)
#:use-module (srfi srfi-1)
+ #:use-module (srfi srfi-9)
+ #:use-module (srfi srfi-9 gnu)
#:use-module (srfi srfi-34)
#:use-module (srfi srfi-35)
#:use-module (ice-9 match)
@@ -55,6 +58,12 @@
openssh-host-host-key-algorithms
openssh-host-accepted-key-types
openssh-host-extra-content
+ proxy-jump
+ proxy-jump-host-name
+ proxy-jump-port
+ proxy-jump-user
+ proxy-command
+ proxy-command->string
home-openssh-service-type
home-ssh-agent-service-type))
@@ -114,6 +123,54 @@
(define-maybe string-list)
+(define-record-type <proxy-command>
+ (proxy-command command)
+ proxy-command?
+ (command proxy-command->string))
+
+(set-record-type-printer! <proxy-command>
+ (lambda (obj port)
+ (format port "#<proxy-command ~s>" (proxy-command->string obj))))
+
+(define-configuration/no-serialization proxy-jump
+ (user
+ maybe-string
+ "User name on the remote host.")
+ (host-name
+ (string)
+ "Host name---e.g., @code{foo.example.org} or @code{192.168.1.2}.")
+ (port
+ maybe-natural-number
+ "TCP port number to connect to."))
+
+(define (proxy-jump->string proxy-jump)
+ (match-record proxy-jump <proxy-jump>
+ (host-name user port)
+ (string-append
+ (if (maybe-value-set? user) (string-append user "@") "")
+ host-name
+ (if (maybe-value-set? port) (string-append ":" (number->string port)) ""))))
+
+(define (proxy-command-or-jump-list? x)
+ (or (proxy-command? x)
+ (and (list? x)
+ (every proxy-jump? x))))
+
+(define (serialize-proxy-command-or-jump-list field value)
+ (if (proxy-command? value)
+ (serialize-string 'proxy-command (proxy-command->string value))
+ (serialize-string-list 'proxy-jump (map proxy-jump->string value))))
+
+(define-maybe proxy-command-or-jump-list)
+
+(define (sanitize-proxy-command properties)
+ (lambda (value)
+ (when (maybe-value-set? value)
+ (warn-about-deprecation 'proxy-command properties #:replacement 'proxy))
+ (unless (maybe-string? value)
+ (configuration-field-error (source-properties->location properties) 'proxy-command value))
+ value))
+
(define-configuration openssh-host
(name
(string)
@@ -155,7 +212,13 @@ machine.")
maybe-string
"The command to use to connect to the server. As an example, a command
to connect via an HTTP proxy at 192.0.2.0 would be: @code{\"nc -X
-connect -x 192.0.2.0:8080 %h %p\"}.")
+connect -x 192.0.2.0:8080 %h %p\"}. Using 'proxy-command' is deprecated, use
+'proxy' instead."
+ (sanitizer (sanitize-proxy-command (current-source-location))))
+ (proxy
+ maybe-proxy-command-or-jump-list
+ "The command to use to connect to the server or a list of SSH hosts to jump
+through before connecting to the server.")
(host-key-algorithms
maybe-string-list
"The list of accepted host key algorithms---e.g.,
diff --git a/gnu/local.mk b/gnu/local.mk
index b7af7726e8..f0d129b493 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -999,6 +999,7 @@ dist_patch_DATA = \
%D%/packages/patches/classpath-aarch64-support.patch \
%D%/packages/patches/classpath-miscompilation.patch \
%D%/packages/patches/cling-use-shared-library.patch \
+ %D%/packages/patches/clog-fix-shared-build.patch \
%D%/packages/patches/clucene-pkgconfig.patch \
%D%/packages/patches/cmake-curl-certificates-3.24.patch \
%D%/packages/patches/coda-use-system-libs.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a986e118f8..68c1406fc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2220,167 +2220,179 @@ easy-to-perform steps.")
(license license:gpl3+)))
(define-public bpp-core
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
- (package
- (name "bpp-core")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-core")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "C++ libraries for Bioinformatics")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-core")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"))))
+ (build-system cmake-build-system)
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html")
+ (synopsis "C++ libraries for Bioinformatics")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-phyl
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
- (package
- (name "bpp-phyl")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ phylogenetic Library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-phyl")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
+ (synopsis "Bio++ phylogenetic library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides phylogenetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
+
+(define-public bpp-phyl-omics
+ (package
+ (name "bpp-phyl-omics")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; No test provided.
+ (inputs
+ (list bpp-core
+ bpp-phyl
+ bpp-seq
+ bpp-seq-omics))
+ (home-page "https://github.com/BioPP/bpp-phyl-omics")
+ (synopsis "Bio++ phylogenetic library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ phylogenetics
+library. It is part of the Bio++ project.")
+ (license license:cecill)))
(define-public bpp-popgen
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
- (package
- (name "bpp-popgen")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ population genetics library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-popgen")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-popgen")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
+ (synopsis "Bio++ population genetics library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides population genetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-seq
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
- (package
- (name "bpp-seq")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-seq")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ sequence library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-seq")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/")
+ (synopsis "Bio++ sequence library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides sequence-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
+
+(define-public bpp-seq-omics
+ (package
+ (name "bpp-seq-omics")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://github.com/BioPP/bpp-seq-omics")
+ (synopsis "Bio++ sequence library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ sequence library.
+It is part of the Bio++ project.")
+ (license license:cecill)))
(define-public bppsuite
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
- (package
- (name "bppsuite")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bppsuite")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (native-inputs
- (list groff man-db texinfo))
- (inputs
- `(("bpp-core" ,bpp-core)
- ("bpp-seq" ,bpp-seq)
- ("bpp-phyl" ,bpp-phyl)
- ("bpp-phyl" ,bpp-popgen)))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bioinformatics tools written with the Bio++ libraries")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bppsuite")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bppsuite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (native-inputs
+ (list groff man-db texinfo))
+ (inputs
+ (list bpp-core bpp-seq bpp-phyl bpp-popgen))
+ (home-page "https://github.com/BioPP")
+ (synopsis "Bioinformatics tools written with the Bio++ libraries")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
package provides command line tools using the Bio++ library.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public blast+
(package
@@ -6021,6 +6033,43 @@ resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public maffilter
+ (package
+ (name "maffilter")
+ (version "1.3.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jydu/maffilter")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "196c16qw82niqqyzi7j1ga1n0zmir73bm26kg04m0i5aq2cpa0ml"))))
+ (build-system cmake-build-system)
+ (arguments (list #:tests? #false)) ;there are none
+ (inputs
+ (list boost
+ bpp-core
+ bpp-phyl
+ bpp-phyl-omics
+ bpp-seq
+ bpp-seq-omics
+ zlib))
+ (home-page "https://jydu.github.io/maffilter/")
+ (synopsis "Multiple alignment format file processor")
+ (description
+ "MafFilter is a program dedicated to the analysis of genome alignments.
+It parses and manipulates @acronym{MAF, multiple alignment format} files as
+well as more simple fasta files. This package can be used to design a
+pipeline as a series of consecutive filters, each performing a dedicated
+analysis. Many of the filters are available, from alignment cleaning to
+phylogeny reconstruction and population genetics analysis. Despite various
+filtering options and format conversion tools, MafFilter can compute a wide
+range of statistics (phylogenetic trees, nucleotide diversity, inferrence of
+selection, etc.).")
+ (license license:gpl3+)))
+
(define-public mafft
(package
(name "mafft")
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 81082ec31d..baa6119078 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm