diff options
| -rw-r--r-- | etc/news.scm | 18 | ||||
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 102 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch | 33 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/version-control.scm | 43 |
6 files changed, 98 insertions, 103 deletions
diff --git a/etc/news.scm b/etc/news.scm index 61334411dd..fa1b76adcf 100644 --- a/etc/news.scm +++ b/etc/news.scm @@ -28,6 +28,7 @@ (entry (commit "c42b7baf13c7633b4512e94da7445299c57b247d") (title (en "New @option{--export-manifest} option for @command{guix shell}") + (de "Neue Option @option{--export-manifest} für @command{guix shell}") (fr "Nouvelle option @option{--export-manifest} de @command{guix shell}")) (body (en "If you use @command{guix shell}, you might wonder how to @@ -44,6 +45,23 @@ guix shell --export-manifest \\ @end lisp Run @code{info \"(guix) Invoking guix shell\"} for more information.") + (de "Wenn Sie @command{guix shell} benutzen, haben Sie sich vielleicht +einmal gefragt, wie Sie eine Befehlszeile in eine Manifest-Datei „übersetzen“ +können, die Sie unter Versionskontrolle stellen können, mit anderen teilen +können und an @command{guix shell -m} oder tatsächlich die meisten anderen +@command{guix}-Befehle übergeben können. Die Antwort ist die neue +Befehlszeilenoption @option{--export-manifest}. + +Zum Beispiel gibt der folgende Befehl ein Manifest mit den genannten Paketen +aus: + +@lisp +guix shell --export-manifest \\ + -D guile git emacs emacs-geiser emacs-geiser-guile +@end lisp + +Führen Sie @command{info \"(guix.de) Aufruf von guix shell\"} aus, um mehr +zu erfahren.") (fr "Si tu utilises @command{guix shell}, tu t'es peut-être déjà demandé comment « traduire » une ligne de commande en un fichier manifeste que tu puisse garder en gestion de version, partager et passer à @command{guix diff --git a/gnu/local.mk b/gnu/local.mk index f5e2702031..420aa91d86 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1627,7 +1627,6 @@ dist_patch_DATA = \ %D%/packages/patches/pidgin-add-search-path.patch \ %D%/packages/patches/pigx-bsseq-no-citeproc.patch \ %D%/packages/patches/pigx-chipseq-no-citeproc.patch \ - %D%/packages/patches/pigx-scrnaseq-no-citeproc.patch \ %D%/packages/patches/pinball-system-ltdl.patch \ %D%/packages/patches/pingus-boost-headers.patch \ %D%/packages/patches/pingus-sdl-libs-config.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eed7e54f7f..e9778831d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11132,7 +11132,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -11140,65 +11140,63 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")) - (patches (search-patches "pigx-scrnaseq-no-citeproc.patch")))) + "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) (build-system gnu-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) - (add-before 'configure 'set-PYTHONPATH + (add-before 'configure 'set-additional-environment-variables (lambda _ + ;; Needed because of loompy + (setenv "NUMBA_CACHE_DIR" "/tmp") + ;; Needed to capture environment (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) - (native-inputs - (list automake autoconf)) (inputs - `(("coreutils" ,coreutils) - ("perl" ,perl) - ("fastqc" ,fastqc) - ("flexbar" ,flexbar) - ("java" ,icedtea-8) - ("jellyfish" ,jellyfish) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-pandas" ,python-pandas) - ("python-magic" ,python-magic) - ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy) - ("pandoc" ,pandoc) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("star" ,star-for-pigx) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-dropbead" ,r-dropbead) - ("r-dt" ,r-dt) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hdf5array" ,r-hdf5array) - ("r-pheatmap" ,r-pheatmap) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rtsne" ,r-rtsne) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-seurat" ,r-seurat) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-yaml" ,r-yaml))) + (list coreutils + perl + fastqc + flexbar + icedtea-8 + jellyfish + python-wrapper + python-pyyaml + python-pandas + python-magic + python-numpy + python-loompy + pandoc + samtools + snakemake + star-for-pigx + r-minimal + r-argparser + r-cowplot + r-data-table + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-dropbead + r-dt + r-genomicalignments + r-genomicfiles + r-genomicranges + r-ggplot2 + r-hdf5array + r-pheatmap + r-rmarkdown + r-rsamtools + r-rtracklayer + r-rtsne + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-stringr + r-yaml)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") - (description "PiGX scRNAseq is an analysis pipeline for preprocessing and + (description + "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are read files from the sequencing experiment, and a configuration file which describes the experiment. It produces processed files for downstream analysis diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch deleted file mode 100644 index 4cce33fb01..0000000000 --- a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_scrnaseq-1.1.7/configure.ac pigx_scrnaseq-1.1.7.patched/configure.ac ---- pigx_scrnaseq-1.1.7/configure.ac 2020-03-17 14:37:46.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/configure.ac 2021-10-06 13:55:49.779271317 +0200 -@@ -43,7 +43,6 @@ - find_or_override_prog([GNUBASH], [bash]) - find_or_override_prog([SNAKEMAKE], [snakemake]) - find_or_override_prog([PANDOC], [pandoc]) --find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc]) - find_or_override_prog([FASTQC], [fastqc]) - find_or_override_prog([STAR], [STAR]) - find_or_override_prog([SAMTOOLS], [samtools]) -diff -Naur pigx_scrnaseq-1.1.7/Makefile.in pigx_scrnaseq-1.1.7.patched/Makefile.in ---- pigx_scrnaseq-1.1.7/Makefile.in 2020-11-30 16:55:48.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/Makefile.in 2021-10-06 13:55:52.224340194 +0200 -@@ -395,7 +395,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PERL = @PERL@ - PYTHON = @PYTHON@ -diff -Naur pigx_scrnaseq-1.1.7/pigx-scrnaseq.in pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in ---- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 2020-11-30 16:08:55.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in 2021-10-06 13:55:47.889218079 +0200 -@@ -274,7 +274,6 @@ - if path.exists(bin): shutil.rmtree(bin) - os.makedirs(bin, exist_ok=True) - os.symlink('@PANDOC@', path.join(bin, "pandoc")) -- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc")) - os.symlink('@RSCRIPT@', path.join(bin, "Rscript")) - os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] - os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f849107cfe..ea643461b9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -203,7 +203,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.1.2") + (version "4.1.3") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -211,7 +211,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "1brqmc7mmb0z94kcs4crgl6v9a6sxhm9fm3y177d81vjkxg24di0")))) + "1mpy4sar1amx5ai9rqr9s0nw8p65iqfrqbm5n9h402b17hrmpzqm")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index bbceea1147..d77c2e51f6 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -32,7 +32,7 @@ ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org> ;;; Copyright © 2020, 2021 Michael Rohleder <mike@rohleder.de> -;;; Copyright © 2021, 2022 Greg Hogan <code@greghogan.com> +;;; Copyright © 2021 Greg Hogan <code@greghogan.com> ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2021 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2021 Léo Le Bouter <lle-bout@zaclys.net> @@ -338,7 +338,8 @@ Python 3.3 and later, rather than on Python 2.") (("uname_S := .*" all) (if (equal? ,(%current-target-system) "i586-pc-gnu") "uname_S := GNU\n" - all)))))) + all))) + #t))) ;; We do not have bash-for-tests when cross-compiling. `((add-after 'unpack 'modify-PATH (lambda* (#:key inputs #:allow-other-keys) @@ -348,24 +349,28 @@ Python 3.3 and later, rather than on Python 2.") ;; similar does the right thing. (setenv "PATH" (string-join (remove (cut string-prefix? bash-full <>) path) - ":"))))))) + ":")) + #t))))) ;; Add cross curl-config script to PATH when cross-compiling. ,@(if (%current-target-system) '((add-before 'configure 'add-cross-curl-config (lambda* (#:key inputs #:allow-other-keys) (setenv "PATH" (string-append (assoc-ref inputs "curl") "/bin:" - (getenv "PATH")))))) + (getenv "PATH"))) + #t))) '()) (add-after 'configure 'patch-makefiles (lambda _ (substitute* "Makefile" (("/usr/bin/perl") (which "perl")) - (("/usr/bin/python") (which "python3"))))) + (("/usr/bin/python") (which "python3"))) + #t)) (add-after 'configure 'add-PM.stamp (lambda _ ;; Add the "PM.stamp" to avoid "no rule to make target". - (call-with-output-file "perl/PM.stamp" (const #t)))) + (call-with-output-file "perl/PM.stamp" (const #t)) + #t)) (add-after 'build 'build-subtree (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "contrib/subtree" @@ -384,7 +389,8 @@ Python 3.3 and later, rather than on Python 2.") (invoke "make" "install") (invoke "make" "install-doc") (substitute* "git-subtree" - (("/bin/sh") (which "sh")))))) + (("/bin/sh") (which "sh")))) + #t)) (add-before 'check 'patch-tests (lambda _ (let ((store-directory (%store-directory))) @@ -422,7 +428,8 @@ Python 3.3 and later, rather than on Python 2.") (for-each delete-file '("t/t9128-git-svn-cmd-branch.sh" "t/t9167-git-svn-cmd-branch-subproject.sh" - "t/t9141-git-svn-multiple-branches.sh"))))) + "t/t9141-git-svn-multiple-branches.sh")) + #t))) (add-after 'install 'install-shell-completion (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -430,7 +437,8 @@ Python 3.3 and later, rather than on Python 2.") ;; TODO: Install the tcsh and zsh completions in the right place. (mkdir-p completions) (copy-file "contrib/completion/git-completion.bash" - (string-append completions "/git"))))) + (string-append completions "/git")) + #t))) (add-after 'install 'install-credential-netrc (lambda* (#:key outputs #:allow-other-keys) (let* ((netrc (assoc-ref outputs "credential-netrc"))) @@ -444,22 +452,24 @@ Python 3.3 and later, rather than on Python 2.") ;; community calls this "dotless @INC"). (wrap-program (string-append netrc "/bin/git-credential-netrc") `("PERL5LIB" ":" prefix - (,(string-append (assoc-ref outputs "out") - "/share/perl5"))))))) + (,(string-append (assoc-ref outputs "out") "/share/perl5")))) + #t))) (add-after 'install 'install-credential-libsecret (lambda* (#:key outputs #:allow-other-keys) (let* ((libsecret (assoc-ref outputs "credential-libsecret"))) (with-directory-excursion "contrib/credential/libsecret" ((assoc-ref gnu:%standard-phases 'build)) (install-file "git-credential-libsecret" - (string-append libsecret "/bin")))))) + (string-append libsecret "/bin")) + #t)))) (add-after 'install 'install-subtree (lambda* (#:key outputs #:allow-other-keys) (let ((subtree (assoc-ref outputs "subtree"))) (install-file "contrib/subtree/git-subtree" (string-append subtree "/bin")) (install-file "contrib/subtree/git-subtree.1" - (string-append subtree "/share/man/man1"))))) + (string-append subtree "/share/man/man1")) + #t))) (add-after 'install 'restore-sample-hooks-shebang (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -468,7 +478,8 @@ Python 3.3 and later, rather than on Python 2.") (format #t "restoring shebang on `~a'~%" file) (substitute* file (("^#!.*/bin/sh") "#!/bin/sh"))) - (find-files dir ".*"))))) + (find-files dir ".*")) + #t))) (add-after 'install 'split (lambda* (#:key inputs outputs #:allow-other-keys) ;; Split the binaries to the various outputs. @@ -544,7 +555,9 @@ Python 3.3 and later, rather than on Python 2.") (wrap-program git-sm `("PATH" ":" prefix (,(string-append (assoc-ref inputs "perl") - "/bin"))))))) + "/bin")))) + + #t))) (add-after 'split 'install-man-pages (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) |