diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 27 |
1 files changed, 18 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c78f017a24..ccee9d1f60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3787,6 +3787,13 @@ UCSC genome browser.") "-xf" (assoc-ref inputs "test-data")) ;; This one requires bowtie-build (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-after 'unpack 'patch-for-python-3.10 + (lambda _ + ;; Some classes were moved from collections to collections.abc + ;; in Python 3.10. + (substitute* "plastid/readers/bigbed.pyx" + ((", Iterable") + "\nfrom collections.abc import Iterable")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. @@ -17809,8 +17816,10 @@ pycisTarget and SCENIC.") (list python-bokeh python-dask python-distributed + python-lz4 python-numpy python-pandas + python-pyarrow python-scikit-learn python-scipy python-tornado-6)) @@ -18413,6 +18422,7 @@ Cflags: -I${includedir}~%" (description "The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.") + (properties `((tunable? . #t))) (license license:expat))) (define-public vcflib @@ -19846,7 +19856,7 @@ sequences") (inputs (list zlib)) (home-page "https://github.com/ACEnglish/bwapy") - (synopsis "Python bindings to bwa alinger") + (synopsis "Python bindings to bwa aligner") (description "This package provides Python bindings to the bwa mem aligner.") ;; These Python bindings are licensed under Mozilla Public License 2.0, @@ -20456,7 +20466,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") (define-public wfmash (package (name "wfmash") - (version "0.8.1") + (version "0.10.5") (source (origin (method url-fetch) @@ -20464,7 +20474,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") version "/wfmash-v" version ".tar.gz")) (sha256 (base32 - "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + "1jsvnnh14h3ir4l13qhmglhd25kzwvni9apgvr1lbikqwgrpkiq4")) (snippet #~(begin (use-modules (guix build utils)) @@ -20475,14 +20485,12 @@ based on the pairwise alignment of hidden Markov models (HMMs).") "<atomic_queue/atomic_queue.h>")) ;; Remove compiler optimizations. (substitute* (find-files "." "CMakeLists\\.txt") - (("-mcx16 ") "") - (("-march=native ") "")) - ;; Allow building on architectures other than x86_64. - (substitute* "src/common/dset64.hpp" - (("!__x86_64__") "0")))))) + (("-march=native ") "")))))) (build-system cmake-build-system) (arguments (list + #:configure-flags + #~(list "-DWFA_PNG_AND_TSV=ON") #:phases #~(modify-phases %standard-phases (replace 'check @@ -20595,7 +20603,8 @@ based on the pairwise alignment of hidden Markov models (HMMs).") jemalloc zlib)) (native-inputs - (list samtools)) + (list pkg-config + samtools)) (synopsis "Base-accurate DNA sequence aligner") (description "@code{wfmash} is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that |