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80547 Commits (20d52562e5c943b30e48e310b58b94054c3a54e5)

Author SHA1 Message Date
Ricardo Wurmus f0f839c124
gnu: r-deepsnv: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0.
[inputs]: Remove zlib.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus dec096f827
gnu: r-decipher: Update to 2.20.0.
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0.
[propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 116df58449
gnu: r-cummerbund: Update to 2.34.0.
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus e6c5d8ce2c
gnu: r-coverageview: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 7bac473d06
gnu: r-biocgenerics: Update to 0.38.0.
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus b05761a5a9
gnu: r-biocversion: Update to 3.13.1.
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 405b386656
gnu: r-aneufinder: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 75817956c1
gnu: r-hdf5array: Update to 1.20.0.
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0.
[arguments]: Remove.
[propagated-inputs]: Add r-rhdf5filters.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus bfa23ec526
gnu: r-cytoml: Update to 2.4.0.
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 764e2dba20
gnu: r-flowworkspace: Update to 4.4.0.
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0.
[arguments]: Remove.
[propagated-inputs]: Add r-delayedarray and r-s4vectors.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus b9751b629c
gnu: r-ncdfflow: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 5c37a048bb
gnu: r-cytolib: Update to 2.4.0.
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0.
[arguments]: Remove.
[native-inputs]: Remove pkg-config.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 782d27f77d
gnu: r-rhdf5: Update to 2.36.0.
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 87d06a725f
gnu: r-mzr: Update to 2.26.0.
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0.
[arguments]: Remove obsolute substitution.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus 5d13aab6ca
gnu: r-msnid: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0.
[arguments]: Set HOME variable.
2021-06-05 09:12:40 +02:00
Ricardo Wurmus d0a7dc0cb6
gnu: r-bioccheck: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0.
[arguments]: Remove.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus 1b0338d76b
gnu: r-rhdf5lib: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.0.
[source]: Update deletions.
[arguments]: Update substitutions.
[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus 53ec97713a
gnu: Add r-metapod.
* gnu/packages/bioconductor.scm (r-metapod): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus 8caab75883
gnu: Add r-ggtree.
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus ab4a91b252
gnu: Add r-treeio.
* gnu/packages/bioconductor.scm (r-treeio): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus fd4fa40ac4
gnu: Add r-scaledmatrix.
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus efefb2be3a
gnu: Add r-trajectoryutils.
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus ce99b4da63
gnu: Add r-restfulr.
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus ab66c9a2cd
gnu: Add r-arrow.
* gnu/packages/cran.scm (r-arrow): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus b71f21339f
gnu: Add r-ggpointdensity.
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus 41ea9bed97
gnu: Add r-ggnewscale.
* gnu/packages/cran.scm (r-ggnewscale): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus d5c08f11e1
gnu: Add r-aplot.
* gnu/packages/cran.scm (r-aplot): New variable.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus c343c3bc1f
guix: Update to Bioconductor 3.13.
* guix/build-system/r.scm (bioconductor-uri): Update version.
* guix/import/cran.scm (%bioconductor-version): Update.
2021-06-05 09:12:39 +02:00
Ricardo Wurmus f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-05 09:12:39 +02:00
Maxim Cournoyer 683eb7c5b1
gnu: Remove remnants of nettle 3.5.
The source of nettle-3.5 was already using the source of nettle-3.7.

* gnu/packages/nettle.scm
(nettle-3.5): Rename to 'nettle'.
(nettle-3.7): Remove variable.
(nettle): Remove alias.
2021-06-05 02:09:03 -04:00
Maxim Cournoyer 5d547f74ed
gnu: nasm: Update to 2.15.05.
* gnu/packages/assembly.scm (nasm): Update to 2.15.05.
[phases]{dont-build-ps-pdf-outputs}: Adjust patching to changes in the source.
2021-06-05 00:14:57 -04:00
Roel Janssen 7382aa00b8
gnu: python-scanpy: Update to 1.7.2.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04 23:51:35 +02:00
Roel Janssen e639da604f
gnu: python-anndata: Update to 0.7.6.
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
2021-06-04 23:51:24 +02:00
Maxime Devos d1827d5c63
gnu: wireguard-tools: Set #:sh argument of 'wrap-program'.
* gnu/packages/vpn.scm
  (wireguard-tools)[arguments]<#:phases>{wrap-wg-quick}:
  Set #:sh argument of ‘wrap-program’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos 96a2ae40fb
gnu: protonvpn-cli: Set #:sh argument of 'wrap-program'.
* gnu/packages/vpn.scm
  (protonvpn-cli)[arguments]<#:phases>{wrap-wrapper}:
  Set #:sh argument of ‘wrap-program’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos b74085ce36
gnu: openconnect-sso: Set #:sh argument of 'wrap-program'.
* gnu/packages/vpn.scm
  (openconnect-sso)[arguments]<#:phases>{wrap-qt-process-path}
  Set #:sh argument of ‘wrap-program’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos 3bbb0ec888
gnu: vpnc-scripts: Set #:guile argument of 'wrap-script'.
* gnu/packages/vpn.scm
  (vpnc-scripts)[arguments]<#:phases>{wrap-scripts}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos a4e38cc216
gnu: clipmenu: Set #:guile argument of 'wrap-script'.
* gnu/packages/xdisorg.scm
  (clipmenu)[arguments]<#:phases>{wrap-script}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos 0758ee8002
gnu: sieve-connect: Set #:guile argument of 'wrap-script'.
* gnu/packages/mail.scm
  (sieve-connect)[arguments]<#:phases>{wrap-program}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'.
* gnu/packages/bioinformatics.scm
  (nanopolish)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
Maxime Devos 2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'.
* gnu/packages/bioinformatics.scm
  (gess)[arguments]<#:phases>{install}
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'.
* gnu/packages/bioinformatics.scm
  (prinseq)[arguments]<#:phases>{install}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'.
* gnu/packages/bioinformatics.scm
  (proteinortho)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos b202fdf131
gnu: bats: Set #:guile argument of 'wrap-script'.
* gnu/packages/bash.scm
  (bats)[arguments]<#:builder>: Set #:guile argument
  of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos 0a843e3643
gnu: carla: Set #:guile argument of 'wrap-script'.
* gnu/packages/audio.scm
  (carla)[arguments]<#:phases>{wrap-executables}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos a62d17dc05
rakudo-build-system: Look up the interpreter in 'inputs'.
* guix/build/rakudo-build-system.scm (wrap): Pass
  the shell interpreter from 'inputs' to 'wrap-program' using
  'search-input-file'.

Partially-Fixes: <https://issues.guix.gnu.org/47869>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos 2ac898d7f8
qt-build-system: Look up the interpreter in 'inputs'.
* guix/build/qt-build-system.scm (wrap-all-programs): Pass
  the shell interpreter from 'inputs' to 'wrap-program' using
  'search-input-file'.

Partially-Fixes: <https://issues.guix.gnu.org/47869>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
Maxime Devos 5b24cbee31
python-build-system: Look up the interpreter in 'inputs'.
* guix/build/python-build-system.scm (wrap): Pass the shell
  interpreter from 'inputs' to 'wrap-program' using 'search-input-file'.

Partially-Fixes: <https://issues.guix.gnu.org/47869>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:31 +02:00
Maxime Devos 1dbc3b2b0c
glib-or-gtk-build-system: Look up the interpreter in 'inputs'.
* guix/build/glib-or-gtk-build-system.scm (wrap-all-programs): Pass
  the shell interpreter from 'inputs' to 'wrap-program' using
  'search-input-file'.

Partially-Fixes: <https://issues.guix.gnu.org/47869>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:31 +02:00
Maxime Devos 5378edeab4
utils: Define ‘search-input-file’ procedure.
The procedure ‘which’ from (guix build utils)
is used for two different purposes:

  1. for finding the absolute file name of a binary
     that needs to run during the build process

  2. for finding the absolute file name of a binary,
     for the target system (as in --target=TARGET),
     e.g. for substituting sh->/gnu/store/.../bin/sh,
     python->/gnu/store/.../bin/python.

When compiling natively (target=#f in Guix parlance),
this is perfectly fine.

However, when cross-compiling, there is a problem.
"which" looks in $PATH for binaries.  That's good for purpose (1),
but incorrect for (2), as the $PATH contains binaries from native-inputs
instead of inputs.

This commit defines a ‘search-input-file’ procedure. It functions
like 'which', but instead of searching in $PATH, it searches in
the 'inputs' of the build phase, which must be passed to
‘search-input-file’ as an argument. Also, the file name must
include "bin/" or "sbin/" as appropriate.

* guix/build/utils.scm (search-input-file): New procedure.
* tests/build-utils.scm
  ("search-input-file: exception if not found")
  ("search-input-file: can find if existent"): Test it.
* doc/guix.texi (File Search): Document it.

Partially-Fixes: <https://issues.guix.gnu.org/47869>
Co-Authored-By: Ludovic Courtès <ludo@gnu.org>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:26 +02:00