diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 231 |
1 files changed, 176 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 341731d066..d47940e0e2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1254,7 +1254,9 @@ libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" (list boost hdf5 htslib pbbam zlib)) (native-inputs (list googletest pkg-config)) - (home-page "https://github.com/PacificBiosciences/blasr_libcpp") + (home-page + (string-append "https://web.archive.org/web/20201106122415/" + "https://github.com/PacificBiosciences/blasr_libcpp")) (synopsis "Library for analyzing PacBio genomic sequences") (description "This package provides three libraries used by applications for analyzing @@ -1296,7 +1298,8 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " (list boost blasr-libcpp hdf5 pbbam zlib)) (native-inputs (list pkg-config)) - (home-page "https://github.com/PacificBiosciences/blasr") + (home-page (string-append "https://web.archive.org/web/20210813124135/" + "https://github.com/PacificBiosciences/blasr")) (synopsis "PacBio long read aligner") (description "Blasr is a genomic sequence aligner for processing PacBio long reads.") @@ -1408,11 +1411,12 @@ Format (GFF) with Biopython integration.") (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) (define-public python-bcbio-gff/biopython-1.73 - (package - (inherit python-bcbio-gff) - (propagated-inputs - (modify-inputs (package-propagated-inputs python-bcbio-gff) - (replace "python-biopython" python-biopython-1.73))))) + (hidden-package + (package + (inherit python-bcbio-gff) + (propagated-inputs + (modify-inputs (package-propagated-inputs python-bcbio-gff) + (replace "python-biopython" python-biopython-1.73)))))) ;; Note: the name on PyPi is "biofluff". (define-public python-biofluff @@ -1676,11 +1680,11 @@ and sequence consensus.") (define-public python-decoupler-py ;; This latest commit fixes a bug in test_omnip.py. - (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace") (revision "1")) (package (name "python-decoupler-py") - (version (git-version "1.3.1" revision commit)) + (version (git-version "1.5.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1689,7 +1693,7 @@ and sequence consensus.") (file-name (git-file-name name version)) (sha256 (base32 - "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + "1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl")))) (build-system pyproject-build-system) (arguments (list @@ -1700,6 +1704,10 @@ and sequence consensus.") " and not test_show_resources" " and not test_get_dorothea" " and not test_get_progeny" + " and not test_get_ksn_omnipath" + ;; XXX module 'omnipath.interactions' has no + ;; attribute 'CollecTRI' + " and not test_get_collectri" ;; XXX This one fails because the "texts" list ;; is empty, so there are no texts to adjust. ;; It is not clear whether this a compatibility @@ -1859,6 +1867,61 @@ protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.") (license license:asl2.0))) +(define-public python-liana-py + (package + (name "python-liana-py") + (version "0.1.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/liana-py") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00lqrmi38wmdpjlcafgmrnkwsbp0yvm2rya6qs8y6jfizww9ff8i")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These tests require internet access. + (string-append "not test_generate_lr_resource" + " and not test_generate_nondefault_lr_resource")) + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable directory to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-anndata + python-cell2cell + python-decoupler-py + python-hypothesis + python-ipykernel + python-ipython + python-mofax + python-mudata + python-nbconvert + python-nbsphinx + python-numpydoc + python-omnipath + python-pandas + python-plotnine + python-pypandoc + python-scipy + python-requests + python-scanpy + python-statsmodels + python-tqdm + tzdata)) + (native-inputs + (list python-black python-pytest python-pytest-cov python-numpy)) + (home-page "https://github.com/saezlab/liana-py") + (synopsis "LIANA is a ligand-receptor analysis framework") + (description "This is a Ligand-Receptor inference framework. The +framework enables the use of any LR method with any resources.") + (license license:gpl3+))) + (define-public python-logomaker (package (name "python-logomaker") @@ -3347,7 +3410,9 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (("inline int map") "int map")))))))) (inputs (list gdsl zlib perl)) - (home-page "http://bwa-pssm.binf.ku.dk/") + ;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are + ;; blank (they actually have "display:none" for some nefarious reason). + (home-page "https://github.com/pkerpedjiev/bwa-pssm") (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") (description "BWA-PSSM is a probabilistic short genomic sequence read aligner based on @@ -4759,17 +4824,15 @@ data and settings.") (list boost cairo rmath-standalone)) (native-inputs (list (texlive-updmap.cfg - (list texlive-cm - texlive-amsfonts - texlive-doi - texlive-fonts-ec - texlive-latex-examplep - texlive-hyperref + (list texlive-doi + texlive-examplep + texlive-forloop + texlive-listofitems texlive-ms - texlive-latex-natbib - texlive-bibtex ;style files used by natbib + texlive-natbib texlive-pgf ;tikz - texlive-latex-verbatimbox)) + texlive-readarray + texlive-verbatimbox)) imagemagick)) (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/") (synopsis "Discover discriminative nucleotide sequence motifs") @@ -4993,6 +5056,54 @@ software to answer ad hoc questions.") go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-baltica + (package + (name "python-baltica") + (version "1.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dieterich-lab/Baltica") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively ".tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-v" "--doctest-modules")))))))) + (propagated-inputs + (list gunicorn + python-anndata + python-click + python-flask + python-flask-wtf + python-h5py + python-numpy + python-psutil + python-pysam + python-pyyaml + python-scipy + snakemake-7)) + (native-inputs (list python-cython python-pyfakefs python-pytest)) + (home-page "https://github.com/dieterich-lab/Baltica") + (synopsis "Integrated splice junction usage analysis") + (description + "This framework facilitates the execution of @dfn{differential junction +usage} (DJU) methods. Additionally, it enables the integration of results from +multiple DJU methods.") + (license license:expat))) + (define-public python-bamnostic (package (name "python-bamnostic") @@ -7273,7 +7384,9 @@ program for nucleotide and protein sequences.") "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) (build-system gnu-build-system) (arguments - '(#:make-flags (list "CFLAGS=-O2 -g -fcommon"))) + `(#:tests? ,(not (or (target-riscv64?) ;XXX: stuck on riscv64-linux + (%current-target-system))) + #:make-flags (list "CFLAGS=-O2 -g -fcommon"))) (inputs ;; XXX: TODO: Enable Lua and Guile bindings. ;; https://github.com/tjunier/newick_utils/issues/13 @@ -8707,7 +8820,7 @@ unique transcripts.") (list ngs-sdk ncbi-vdb file - fuse + fuse-2 hdf5-1.10 libxml2 zlib @@ -9826,6 +9939,14 @@ differently labelled data.") (base32 "04kr1b28p5j7h48g32cldkg87xcmxnmd4kspygkfs7a4amihpi66")))) (properties `((upstream-name . "Pando"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'loosen-requirements + (lambda _ + (substitute* "DESCRIPTION" + ((" \\(==.*,") ","))))))) (propagated-inputs (list r-bayestestr r-foreach @@ -12088,16 +12209,15 @@ programs for inferring phylogenies (evolutionary trees).") (list automake autoconf openmpi - (texlive-updmap.cfg (list texlive-amsfonts - texlive-caption - texlive-cite - texlive-fancyvrb - texlive-fonts-ec - texlive-graphics - texlive-grfext - texlive-hyperref - texlive-latex-psfrag - texlive-xcolor)))) + (texlive-updmap.cfg + (list texlive-caption + texlive-cite + texlive-fancyvrb + texlive-infwarerr + texlive-kvoptions + texlive-pdftexcmds + texlive-psfrag + texlive-xcolor)))) (home-page "https://github.com/stephaneguindon/phyml") (synopsis "Programs for working on SAM/BAM files") (description @@ -17051,32 +17171,33 @@ to an artifact/contaminant file.") (delete-file-recursively "third-party"))))) (build-system gnu-build-system) (arguments - `(#:make-flags '("OPENMP=t") - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-zlib-include - (lambda _ - (substitute* "src/binarySequences.c" - (("../third-party/zlib-1.2.3/zlib.h") "zlib.h")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (doc (string-append out "/share/doc/velvet"))) - (mkdir-p bin) - (mkdir-p doc) - (install-file "velveth" bin) - (install-file "velvetg" bin) - (install-file "Manual.pdf" doc) - (install-file "Columbus_manual.pdf" doc))))))) + (list + #:make-flags #~(list "OPENMP=t") + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-zlib-include + (lambda _ + (substitute* "src/binarySequences.c" + (("../third-party/zlib-1.2.3/zlib.h") "zlib.h")))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin")) + (doc (string-append #$output "/share/doc/velvet"))) + (mkdir-p bin) + (mkdir-p doc) + (install-file "velveth" bin) + (install-file "velvetg" bin) + (install-file "Manual.pdf" doc) + (install-file "Columbus_manual.pdf" doc))))))) (inputs (list openmpi zlib)) (native-inputs - `(("texlive" ,(texlive-updmap.cfg (list texlive-graphics - texlive-fonts-ec - texlive-hyperref))))) + (list (texlive-updmap.cfg + (list texlive-infwarerr + texlive-kvoptions + texlive-pdftexcmds)))) (home-page "https://www.ebi.ac.uk/~zerbino/velvet/") (synopsis "Nucleic acid sequence assembler for very short reads") (description |