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authorRicardo Wurmus <rekado@elephly.net>2024-01-19 23:47:54 +0100
committerRicardo Wurmus <rekado@elephly.net>2024-01-19 23:55:43 +0100
commit74ce9d7e3b0c94b8a5ba1c6159ba15c5787e2094 (patch)
tree00b6d5b668c76833edf8d9a2caea645b09e75def /gnu/packages
parent1d56a2450964a6681f07596feb674d661509e334 (diff)
downloadguix-74ce9d7e3b0c94b8a5ba1c6159ba15c5787e2094.tar.gz
guix-74ce9d7e3b0c94b8a5ba1c6159ba15c5787e2094.zip
gnu: Add r-trna.
* gnu/packages/bioconductor.scm (r-trna): New variable. Change-Id: Ifce902910fa75ddc471d8a25cc974307c19fd1d0
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b1cd1f22cd..80b31e5f17 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11249,6 +11249,43 @@ includes a function to create a cluster-level minimum spanning tree and data
structures to hold pseudotime inference results.")
(license license:gpl3)))
+(define-public r-trna
+ (package
+ (name "r-trna")
+ (version "1.20.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tRNA" version))
+ (sha256
+ (base32
+ "0mcpql3zf1gw2k6gfyqycycc8li00818gd9qzs8s3wva7kxbpn89"))))
+ (properties
+ `((upstream-name . "tRNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biostrings
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-modstrings
+ r-s4vectors
+ r-scales
+ r-stringr
+ r-structstrings
+ r-xvector))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/tRNA")
+ (synopsis "Analyzing tRNA sequences and structures")
+ (description
+ "The tRNA package allows tRNA sequences and structures to be accessed and
+used for subsetting. In addition, it provides visualization tools to compare
+feature parameters of multiple tRNA sets and correlate them to additional
+data. The tRNA package uses GRanges objects as inputs requiring only few
+additional column data sets.")
+ (license license:gpl3)))
+
(define-public r-scds
(package
(name "r-scds")
75a75b20090253613a7a8800d8'>git: Require Guile-Git 0.3.0 or later....* guix/git.scm (auth-supported?): Remove. (clone*): Inline code that was dependent on AUTH-SUPPORTED?. (update-cached-checkout): Likewise. (resolve-reference): Remove check for 'object-lookup-prefix' and use it unconditionally. (load-git-submodules): Remove. (update-submodules): Use 'repository-submodules', 'submodule-lookup', etc. unconditionally. (update-cached-checkout): Use 'repository-close!' unconditionally. * m4/guix.m4 (GUIX_CHECK_GUILE_GIT): New macro. * configure.ac: Use it and error out when it fails. * doc/guix.texi (Requirements): Bump to Guile-Git 0.3.0. Ludovic Courtès 2020-10-05build: Use a 'guile' executable that doesn't warn about locales....This gets rid of: guile: warning: failed to install locale when running the 'guix' command on a foreign distro where 'GUIX_LOCPATH' isn't set. * Makefile.am (pkglibexec_PROGRAMS, guile_SOURCES, guile_LDADD) (guile_CFLAGS): New variables. (install-exec-hook): New target. (AUX_FILES): Remove 'guile-launcher.c'. * configure.ac: Use 'GUILE_FLAGS'. Ludovic Courtès 2020-08-29build: Remove references to the 'nix-hash' program....* configure.ac: Remove check for 'nix-hash'. * tests/base32.scm (%nix-hash, %have-nix-hash?): Remove. ("sha256 & bytevector->nix-base32-string"): Remove test. * build-aux/pre-inst-env.in: Do not set 'NIX_HASH' environment variable. Ludovic Courtès 2020-08-29build: Remove check for Guile 2.2.1 bug....This check is unnecessary since e688c2df3924423b67892cc9939ca099c729d1cb. * m4/guix.m4 (GUIX_ASSERT_SYNTAX_OBJECT_EQUAL): Remove. * configure.ac: Remove user. Ludovic Courtès 2020-08-24Use "guile-zlib" and "guile-lzlib" instead of (guix config)....* Makefile.am (MODULES): Remove guix/zlib.scm and guix/lzlib.scm, (SCM_TESTS): remove tests/zlib.scm, tests/lzlib.scm. * build-aux/build-self.scm (make-config.scm): Remove unused %libz variable. * configure.ac: Remove LIBZ and LIBLZ variables and check instead for Guile-zlib and Guile-lzlib. * doc/guix.texi ("Requirements"): Remove zlib requirement and add Guile-zlib and Guile-lzlib instead. * gnu/packages/package-management.scm (guix)[native-inputs]: Add "guile-zlib" and "guile-lzlib", [inputs]: remove "zlib" and "lzlib", [propagated-inputs]: ditto, [arguments]: add "guile-zlib" and "guile-lzlib" to Guile load path. * guix/config.scm.in (%libz, %liblz): Remove them. * guix/lzlib.scm: Remove it. * guix/man-db.scm: Use (zlib) instead of (guix zlib). * guix/profiles.scm (manual-database): Do not stub (guix config) in imported modules list, instead add "guile-zlib" to the extension list. * guix/scripts/publish.scm: Use (zlib) instead of (guix zlib) and (lzlib) instead of (guix lzlib), (string->compression-type, effective-compression): do not check for zlib and lzlib availability. * guix/scripts/substitute.scm (%compression-methods): Do not check for lzlib availability. * guix/self.scm (specification->package): Add "guile-zlib" and "guile-lzlib" and remove "zlib" and "lzlib", (compiled-guix): remove "zlib" and "lzlib" arguments and add guile-zlib and guile-lzlib to the dependencies, also do not pass "zlib" and "lzlib" to "make-config.scm" procedure, (make-config.scm): remove "zlib" and "lzlib" arguments as well as %libz and %liblz variables. * guix/utils.scm (lzip-port): Use (lzlib) instead of (guix lzlib) and do not check for lzlib availability. * guix/zlib.scm: Remove it. * m4/guix.m4 (GUIX_LIBZ_LIBDIR, GUIX_LIBLZ_FILE_NAME): Remove them. * tests/lzlib.scm: Use (zlib) instead of (guix zlib) and (lzlib) instead of (guix lzlib), and do not check for zlib and lzlib availability. * tests/publish.scm: Ditto. * tests/substitute.scm: Do not check for lzlib availability. * tests/utils.scm: Ditto. * tests/zlib.scm: Remove it. Mathieu Othacehe 2020-06-16etc: Add committer script....* etc/committer.scm.in: New file. * configure.ac: Configure it. Ricardo Wurmus 2020-05-28maint: Check whether Guile-Gcrypt is recent enough....Suggested by Danny Milosavljevic <dannym@scratchpost.org> in <https://bugs.gnu.org/41494>. * m4/guix.m4 (GUIX_CHECK_GUILE_GCRYPT): New macro. * configure.ac: Use it. Ludovic Courtès 2020-05-14etc: indent-code.el: Use the --quick option....This prevents Emacs from loading the autoload definitions found in its profile, which needlessly clutters the output. It also prevents Geiser (if installed) from blocking the script and asking the user to input the Scheme implementation to use. The trick for passing multiple arguments to Emacs is to use what is called a "sesquicolon" (see https://www.emacswiki.org/emacs/EmacsScripts). * etc/indent-code.el.in: Rename to... * etc/indent-code.el: ...this. Adapt the shebang to use a sesquicolon, and pass the --quick option to Emacs. Since this line is interpreted by the shell, simply use Emacs from the PATH instead of from a hard coded location. (main): New procedure, used as the entry point. * configure.ac: Remove the warning about Emacs. Emacs can now be installed any time by the user if they want to use the script. * .gitignore: No longer ignore changes to etc/indent-code.el. Maxim Cournoyer 2020-04-23build: Don't build man pages when cross-compiling....* configure.ac: Define 'CROSS_COMPILING' Automake conditional. * doc/local.mk (dist_man1_MANS): Wrap in "if !CROSS_COMPILING". Ludovic Courtès 2020-03-11build: Require Guile 2.2.3 or later....* configure.ac: For 2.2.x, require 2.2.3 or later. Ludovic Courtès 2020-01-17build: Allow builds with Guile 3.0....* configure.ac: Add "3.0" in 'GUILE_PKG' invocation. * doc/guix.texi (Requirements): Mention 3.0.x. Ludovic Courtès 2019-11-09build: Warn about etc/indent-code.el when Emacs is absent....* configure.ac: Warn when 'emacs' is not found, and emit 'etc/indent-code.el' otherwise. Signed-off-by: Ludovic Courtès <ludo@gnu.org> zimoun