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authorRicardo Wurmus <rekado@elephly.net>2021-04-28 10:49:03 +0200
committerRicardo Wurmus <rekado@elephly.net>2021-04-28 10:52:12 +0200
commit5ea5ea60669a398c5c7eaf4cc23f1ec315eb3a3d (patch)
treee914e85801c54b6983513572f7f33c23a949c4f0 /gnu/packages/bioinformatics.scm
parent562c3a4e12b305bb549ed920d0954d9018f158eb (diff)
downloadguix-5ea5ea60669a398c5c7eaf4cc23f1ec315eb3a3d.tar.gz
guix-5ea5ea60669a398c5c7eaf4cc23f1ec315eb3a3d.zip
gnu: Add python-pyliftover.
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm25
1 files changed, 25 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b6e7249980..97f3f916c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15238,6 +15238,31 @@ database. That database maps k-mers to the lowest common ancestor (LCA) of all
genomes known to contain a given k-mer.")
(license license:expat)))
+(define-public python-pyliftover
+ (package
+ (name "python-pyliftover")
+ (version "0.4")
+ ;; The version of pypi does not include test data.
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/konstantint/pyliftover")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1j8jp9iynv2l3jv5pr0pn0p3azlama1bqg233piglzm6bqh3m2m3"))))
+ (build-system python-build-system)
+ (arguments `(#:tests? #false)) ; the tests access the web
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/konstantint/pyliftover")
+ (synopsis "Python implementation of UCSC liftOver genome coordinate conversion")
+ (description
+ "PyLiftover is a library for quick and easy conversion of genomic (point)
+coordinates between different assemblies.")
+ (license license:expat)))
+
(define-public r-signac
(let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
(revision "1"))
='2023-03-09 15:10:13 +0200'>2023-03-09gnu: make-openbios-package: Enable setting configure-flags....* gnu/packages/firmware.scm (make-openbios-package)[arguments]: Adjust custom 'configure phase to apply configure-flags. Efraim Flashner 2023-02-20gnu: make-openbios-package: Update to 1.1-1.af97fd7....* gnu/packages/firmware.scm (make-openbios-package): Update to 1.1-1.af97fd7. [source]: Remove patch. [native-inputs]: Build with gcc-10. Add fcode-utils. * gnu/packages/patches/openbios-gcc-warnings.patch: Remove file. * ngu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner 2023-02-20gnu: Add fcode-utils....* gnu/packages/firmware.scm (fcode-utils): New variable. Efraim Flashner 2023-02-08gnu: sgabios: Don't build for a specific target....* gnu/packages/firmware.scm (sgabios)[arguments]: Set target to #f since we're building a firmware file. Efraim Flashner 2023-02-08gnu: seabios: Don't build for a specific target....* gnu/packages/firmware.scm (seabios)[arguments]: Set target to #f since we're producing a firmware file. Efraim Flashner 2023-02-08gnu: openbios-qemu-ppc: Don't build for a specific target....* gnu/packages/firmware.scm (openbios-qemu-ppc)[arguments]: Set target to #f since we're producing a firmware file and not a binary. Efraim Flashner 2023-02-08gnu: openbios-qemu-ppc: Fix building on aarch64-linux....* gnu/packages/firmware.scm (openbios-qemu-ppc)[arguments]: When building from aarch64-linux build for armhf-linux. Efraim Flashner 2023-01-18gnu: make-arm-trusted-firmware: Simplify build....Reuse knowledge from recent U-Boot modifications to streamline the package definition. * gnu/packages/firmware.scm (make-arm-trusted-firmware): Change optional argument ARCH to keyword TRIPLET. Default to aarch64-linux-gnu. [arguments]: Use gexps. Add a #:target argument. Streamline how the CROSS_COMPILE make flag is computed. [native-inputs]: Delete field. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Maxim Cournoyer 2023-01-13gnu: ovmf-arm: Fix syntax error on armhf-linux....* gnu/packages/firmware.scm (ovmf-arm)[arguments]: Don't add an empty set-env phase when building for armhf-linux. Marius Bakke 2023-01-13gnu: ovmf-aarch64: Fix syntax error on aarch64-linux....* gnu/packages/firmware.scm (ovmf-aarch64)[arguments]: Don't add an empty set-env phase when building for aarch64. Marius Bakke 2023-01-05gnu: ath9k-htc-firmware: Fix deprecation warnings....* gnu/packages/firmware.scm (ath9k-htc-firmware): Invoke cross-binutils using keyword arguments. Maxim Cournoyer 2022-12-25gnu: Add opensbi-qemu....* gnu/packages/firmware.scm (opensbi-qemu): New variable. Marius Bakke 2022-12-25gnu: opensbi: Use the same source file name regardless of variant....* gnu/packages/firmware.scm (make-opensbi-package)[source](file-name): Don't use the NAME variable which changes depending on the variant. Marius Bakke 2022-12-25gnu: Add openbios-qemu-ppc....* gnu/packages/firmware.scm (make-openbios-package): New procedure. (openbios-qemu-ppc): New variable. * gnu/packages/patches/openbios-gcc-warnings.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Marius Bakke 2022-12-23gnu: sgabios: Fix build on cross-build architectures....* gnu/packages/firmware.scm (sgabios)[arguments]: When cross-building add a make-flag to use the correct objcopy. Efraim Flashner 2022-12-22gnu: Add sgabios....* gnu/packages/firmware.scm (sgabios): New variable. Marius Bakke 2022-12-22gnu: Install QEMU firmare files to 'share/qemu'....This paves the way for using a native search path in the future. * gnu/packages/bootloaders.scm (ipxe-qemu)[arguments]: Install firmware files to 'share/qemu' instead of 'share/firmware'. * gnu/packages/firmware.scm (seabios-qemu)[arguments]: Likewise. * gnu/packages/virtualization.scm (qemu)[arguments]: Adjust accordingly. Marius Bakke 2022-12-22gnu: SeaBIOS: Split QEMU variants out to separate package....* gnu/packages/firmware.scm (seabios)[arguments]: Move custom build and install phases out to ... (seabios-qemu): ... this new variable. * gnu/packages/virtualization.scm (qemu)[inputs]: Change from SEABIOS to SEABIOS-QEMU. Marius Bakke 2022-12-21gnu: seabios: Enable for all architectures....* gnu/packages/firmware.scm (seabios)[native-inputs]: When not building from an i686-linux or x86_64-linux machine add cross-gcc and cross-binutils for i686-linux-gnu. [arguments]: When not building from an i686-linux or x86_64-linux machine adjust the Makefile to find the cross build tools needed. [supported-architectures]: Remove field. Efraim Flashner 2022-12-20gnu: seabios: Limit to i686-linux and x86_64-linux....* gnu/packages/firmware.scm (seabios)[supported-systems]: New field. Efraim Flashner 2022-12-20gnu: Add edk2-tools....* gnu/packages/firmware.scm (edk2-tools): New variable. Marius Bakke 2022-12-19gnu: SeaBIOS: Prettify version string....* gnu/packages/firmware.scm (seabios)[arguments]: Display version as "1.16.1/GNU Guix" instead of "1.16.1-guix". Marius Bakke 2022-12-19gnu: SeaBIOS: Build in parallel....* gnu/packages/firmware.scm (seabios)[arguments]: Use N-PAR-FOR-EACH to build the various targets. Marius Bakke 2022-12-19gnu: SeaBIOS: Build more BIOSen....* gnu/packages/firmware.scm (seabios)[arguments]: Build the "128k" and "microvm" BIOSen expected by QEMU. Fix installation of vgabios. Marius Bakke 2022-12-19gnu: SeaBIOS: Remove pre-generated code....* gnu/packages/firmware.scm (seabios)[source](modules, snippet): New fields. [native-inputs]: Add ACPICA. [arguments]: Add build-iasl phase. Marius Bakke 2022-12-19gnu: SeaBIOS: Use G-expression....* gnu/packages/firmware.scm (seabios)[arguments]: Rewrite as gexp. Marius Bakke 2022-12-17gnu: SeaBIOS: Simplify build....* gnu/packages/firmware.scm (seabios)[arguments]: Don't install bios.bin twice. Drop redundant append step. Marius Bakke 2022-12-17gnu: SeaBIOS: Build verbosely....* gnu/packages/firmware.scm (seabios)[arguments]: Add "V=1" to #:make-flags. Marius Bakke 2022-12-17gnu: SeaBIOS: Update to 1.16.1....* gnu/packages/firmware.scm (seabios): Update to 1.16.1. Marius Bakke 2022-11-24gnu: arm-trusted-firmware: Remove blobs in a snippet....* gnu/packages/firmware.scm (make-arm-trusted-firmware)[source]: Add snippet to remove binary blobs. [arguments]: Remove related phase. Efraim Flashner 2022-11-24gnu: arm-trusted-firmware: Update to 2.8....* gnu/packages/firmware.scm (make-arm-trusted-firmware): Update to 2.8. [arguments]: Remove trailing #t from phases. Clean up regexes. Efraim Flashner 2022-11-21gnu: fwupd: Move some inputs to propagated-inputs....* gnu/packages/firmware.scm (fwupd)[propagated-inputs]: Move curl, gcab, glib, gusb, libarchive, gnutls, json-glib and libjcat here from inputs. Signed-off-by: Marius Bakke <marius@gnu.org> Petr Hodina 2022-09-01gnu: fwupd: Disable remotes by default....* gnu/packages/firmware.scm (fwupd) [configure-flags]: Add "-Dlvfs=disabled". [phases]{ensure-all-remotes-are-disabled}: New phase. Maxim Cournoyer 2022-08-31gnu: Add fwupd....* gnu/packages/firmware.scm (fwupd): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Petr Hodina 2022-08-14gnu: Remove ‘open source’ from package descriptions....Also do some (trivial) editing where appropriate. * gnu/packages/bioconductor.scm (r-anaquin, r-rcppnumerical) [description]: Remove superfluous ‘open source’. * gnu/packages/debian.scm (apt-mirror)[description]: Likewise. Add @acronym{}. Drop obscure Ubuntu for famous Trisquel. Reorder. * gnu/packages/documentation.scm (scrollkeeper)[description]: Remove superfluous ‘open systems’. Keep ‘Open Source’ in standard name. * gnu/packages/engineering.scm (freecad, cura-engine)[description]: Remove superfluous ‘open source’ and excessive puffery. * gnu/packages/firmware.scm (make-opensbi-package) [synopsis]: Remove ‘Open Source’. Use @acronym{}. [description]: Fix first sentence to follow guidelines. Use @acronym{}. * gnu/packages/game-development.scm (ioquake3, recastnavigation): [description]: Remove ‘open source’. * gnu/packages/graphics.scm (skia)[description]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-s-sysdeps)[description]: Likewise. * gnu/packages/machine-learning.scm (onnx)[description]: Likewise. Use @acronym{}. * gnu/packages/ocaml.scm (ocaml-cudf)[description]: Likewise. Tobias Geerinckx-Rice