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* gnu: salmon: Use older version of TBB.Ricardo Wurmus2021-10-19
| | | | | | * gnu/packages/bioinformatics.scm (salmon)[arguments]: Define HAVE_NUMERIC_LIMITS128; compute TBB_VERSION. [inputs]: Replace tbb with tbb-for-salmon.
* Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe2021-10-12
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| * gnu: clipper: Disable non-deterministic test.Felix Gruber2021-10-12
| | | | | | | | | | | | | | | | | | This test fails/succeeds non-deterministically. * gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable non-deterministic test test_get_FDR_cutoff_mean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
| * gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
| * gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
| * gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it. [native-inputs]: Add automake/autoconf.
| * gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | * gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
| * gnu: ngless: Fix build.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | | | Apply upstream patch to restore compatibility with current Stackage. * gnu/packages/patches/ngless-unliftio.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/bioinformatics.scm (ngless): Use it.
| * gnu: Update Haskell ecosystem.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bump packages’ versions to the lastest Stackage or Hackage release. Since packages are interdependent, do so in a single commit. 525 packages have been updated. These packages have been removed, because they fail to build, have no newer version available and no dependencies: corrode ghc-easytest ghc-edisonapi ghc-edisoncore ghc-pandoc-types ghc-regex-tdfa-text These have been removed, because they are no longer required: ghc-happy-1.19.9 ghc-prettyprinter-1.6 ghc-protolude-0.3 ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc does not use them any more. Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
| * gnu: pigx-chipseq: Update to 0.0.53.Ricardo Wurmus2021-09-29
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53. [inputs]: Add r-hexbin.
| * gnu: Update some packages using old JavaScript minifier.Charles2021-09-22
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/minetest.scm (minetest-basic-trains): New variable. * gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input. * gnu/packages/ci.scm (laminar): Update uglifyjs input. * gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input. * gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| * gnu: Add r-presto.zimoun2021-09-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-presto): New variable.
| * gnu: discrover: Update package name in texlive-union.Ricardo Wurmus2021-09-13
| | | | | | | | | | * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace texlive-fonts-cm with texlive-cm.
* | Merge branch 'master' into core-updates-frozenLudovic Courtès2021-09-07
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| * gnu: Add megadepth.Ricardo Wurmus2021-09-06
| | | | | | | | * gnu/packages/bioinformatics.scm (megadepth): New variable.
| * gnu: Add r-catch.Ricardo Wurmus2021-09-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-catch): New variable.
| * gnu: Add scregseg.Ricardo Wurmus2021-08-31
| | | | | | | | * gnu/packages/bioinformatics.scm (scregseg): New variable.
| * gnu: python-strawc: Propagate pybind11.Ricardo Wurmus2021-08-31
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from here... [propagated-inputs]: ...to here.
| * gnu: python-scanpy: Propagate sinfo.Ricardo Wurmus2021-08-31
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move python-sinfo from here... [propagated-inputs]: ...to here.
| * gnu: Add python-coolbox.Ricardo Wurmus2021-08-30
| | | | | | | | * gnu/packages/bioinformatics.scm (python-coolbox): New variable.
| * gnu: python-scanpy: Update to 1.8.1.Ricardo Wurmus2021-08-30
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1. [arguments]: Bulid with flit; update list of broken tests. [native-inputs]: Add python-flit and python-anndata:source.
| * gnu: Add python-dna-features-viewer.Ricardo Wurmus2021-08-30
| | | | | | | | * gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
| * gnu: Add python-pybbi.Ricardo Wurmus2021-08-30
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pybbi): New variable.
| * gnu: Add python-strawc.Ricardo Wurmus2021-08-27
| | | | | | | | * gnu/packages/bioinformatics.scm (python-strawc): New variable.
| * gnu: Add r-cytonorm.Ricardo Wurmus2021-08-27
| | | | | | | | * gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
| * gnu: Add ivar.Ricardo Wurmus2021-08-25
| | | | | | | | * gnu/packages/bioinformatics.scm (ivar): New variable.
| * gnu: fastp: Update to 0.20.1.Ricardo Wurmus2021-08-20
| | | | | | | | | | * gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1. [arguments]: Set PREFIX instead of BINDIR.
| * gnu: pigx-rnaseq: Update to 0.0.19.Ricardo Wurmus2021-08-13
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
* | gnu: Use the non-deprecated TeX packages.Ludovic Courtès2021-09-06
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This commit leaves 'dblatex' and 'texlive-hyperref' as users of deprecated packages, but these have many dependents. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use non-deprecated TeX Live packages. (velvet)[native-inputs]: Likewise. * gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise. (chez-web)[native-inputs]: Likewise. * gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise. * gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise. * gnu/packages/maths.scm (hypre)[native-inputs]: Likewise. * gnu/packages/music.scm (lilypond)[native-inputs]: Likewise. * gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise. * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Likewise. (python-matplotlib-documentation)[native-inputs]: Likewise. (python-ipython-documentation)[native-inputs]: Likewise. (python-nbconvert)[native-inputs]: Likewise. (python-pypandoc)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise. * gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise. (teximpatient)[native-inputs]: Likewise. (texlive-latex-pgf)[propagated-inputs]: Likewise. (texlive-beamer)[propagated-inputs]: Likewise.
* | gnu: Replace PYTHONPATH with GUIX_PYTHONPATH.Felix Gruber2021-09-06
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | In packages that do not use python-build-system, PYTHONPATH is generally not defined. Instead we can use GUIX_PYTHONPATH which should contain all Python dependencies. * gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace PYTHONPATH with GUIX_PYTHONPATH. * gnu/packages/debug.scm (c-vise)[arguments]: Idem. * gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem. * gnu/packages/music.scm (a2jmidid)[arguments]: Idem. * gnu/packages/syndication.scm (gfeeds)[arguments]: Idem. * gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* | Merge branch 'master' into core-updates-frozenMarius Bakke2021-08-12
|\| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Conflicts: gnu/packages/algebra.scm gnu/packages/games.scm gnu/packages/golang.scm gnu/packages/kerberos.scm gnu/packages/mail.scm gnu/packages/python.scm gnu/packages/ruby.scm gnu/packages/scheme.scm gnu/packages/tex.scm gnu/packages/tls.scm gnu/packages/version-control.scm
| * gnu: pigx-rnaseq: Update to 0.0.18.Ricardo Wurmus2021-08-11
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
| * gnu: pigx-sars-cov2-ww: Update to 0.0.3.Ricardo Wurmus2021-08-05
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
| * gnu: Add r-spectre.Ricardo Wurmus2021-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-spectre): New variable.
* | Merge branch 'master' into core-updates-frozenMarius Bakke2021-07-29
|\| | | | | | | | | | | | | | | | | | | | | | | | | | | Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
| * gnu: Add seqan 3.Ricardo Wurmus2021-07-26
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (seqan): Rename this variable... (seqan-2): ...to this. (seqan): New variable for seqan3. (flexbar)[native-inputs]: Update name for seqan 2.
| * gnu: Add segemehl.Ricardo Wurmus2021-07-26
| | | | | | | | * gnu/packages/bioinformatics.scm (segemehl): New variable.
| * gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner2021-07-22
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
| * gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner2021-07-22
| | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Replace htslib-1.9 with 1.10. [native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10, bcftools-1.9 with 1.10. (bcftools-1.9): Replace with bcftools-1.10. [native-inputs]: Replace htslib-1.9 with 1.10. (samtools-1.9): Replace with samtools-1.10. [inputs]: Replace htslib-1.9 with 1.10.
| * gnu: Add htslib-1.10.Efraim Flashner2021-07-22
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
| * gnu: python-biopython: Update to 1.73.Efraim Flashner2021-07-22
| | | | | | | | * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
| * gnu: Add r-battenberg.Lars-Dominik Braun2021-07-21
| | | | | | | | * gnu/packages/bioinformatics.scm (r-battenberg): New variable.
| * gnu: Add r-ascat.Lars-Dominik Braun2021-07-21
| | | | | | | | * gnu/packages/bioinformatics.scm (r-ascat): New variable.
| * gnu: Add nanosv.Lars-Dominik Braun2021-07-21
| | | | | | | | * gnu/packages/bioinformatics.scm (nanosv): New variable.
| * gnu: Add python-pyvcf.Lars-Dominik Braun2021-07-21
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
| * gnu: checkm: Rename and update to 1.1.3.Lars-Dominik Braun2021-07-21
| | | | | | | | | | | | | | | | | | | | | | Renamed from python2-checkm-genome to checkm to better reflect its status as standalone-application and support for Python 3. * gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to… (checkm): …here and update to 1.1.3. [propagated-inputs]: Move to inputs. [inputs]: Use Python 3 dependencies. [home-page]: Point to real home-page.
| * gnu: Add tombo.Lars-Dominik Braun2021-07-21
| | | | | | | | * gnu/packages/bioinformatics.scm (tombo): New variable.
* | gnu: Use 'search-input-directory' and 'search-input-file' where appropriate.Ludovic Courtès2021-07-24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This changes some of the remaining uses of this idiom: (string-append (assoc-ref inputs "LABEL") "FILE") to one of: (search-input-file inputs "FILE") (search-input-directory inputs "FILE") * gnu/packages/axoloti.scm (axoloti-patcher): Use 'search-input-directory'. (axoloti-patcher-next): Likewise. * gnu/packages/bioinformatics.scm (java-picard): Likewise. * gnu/packages/bootloaders.scm (grub-hybrid): Likewise. (u-boot-puma-rk3399): Likewise. (u-boot-rock64-rk3328): Likewise. (u-boot-firefly-rk3399): Likewise. (u-boot-rockpro64-rk3399): Likewise. (u-boot-pinebook-pro-rk3399): Likewise. * gnu/packages/cran.scm (r-shiny): Likewise. (r-shinytree): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise. (emacs-rime): Likewise. * gnu/packages/emulators.scm (dolphin-emu): Likewise. * gnu/packages/games.scm (bsd-games): Likewise. (seahorse-adventures): Likewise. (einstein): Likewise. * gnu/packages/gimp.scm (gimp-fourier): Likewise. * gnu/packages/gnome.scm (gspell): Likewise. * gnu/packages/guile-xyz.scm (guile-libyaml): Likewise. * gnu/packages/java.scm (icedtea-7): Likewise. * gnu/packages/language.scm (nimf): Likewise. * gnu/packages/lxde.scm (spacefm): Likewise. * gnu/packages/mail.scm (claws-mail): Likewise. * gnu/packages/netpbm.scm (netpbm): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/scheme.scm (scm): Likewise. * gnu/packages/security-token.scm (python-fido2): Likewise. * gnu/packages/syndication.scm (rtv): Likewise. * gnu/packages/tls.scm (acme-client): Likewise. * gnu/packages/web.scm (netsurf): Likewise. * gnu/packages/wine.scm (wine-staging): Likewise. * gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
* | gnu: Use 'search-input-file' when looking for .jar files.Ludovic Courtès2021-07-24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113): Use 'search-input-file' when looking for *.jar. (fastqc): Likewise. * gnu/packages/groovy.scm (groovy): Likewise. * gnu/packages/java.scm (ant-bootstrap): Likewise. (ecj-bootstrap): Likewise. (java-cisd-base): Likewise. (java-cisd-args4j): Likewise. (java-cisd-jhdf5): Likewise. (java-native-access): Likewise. (java-native-access-platform): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise.
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