diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 139 |
1 files changed, 123 insertions, 16 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 34e8565788..51640b710f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1680,11 +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 @@ -1693,7 +1693,7 @@ and sequence consensus.") (file-name (git-file-name name version)) (sha256 (base32 - "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + "1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl")))) (build-system pyproject-build-system) (arguments (list @@ -1704,6 +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 @@ -1863,6 +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") @@ -4997,6 +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") @@ -7077,22 +7184,22 @@ sequences).") #:make-flags (list "CC=gcc") #:phases (modify-phases %standard-phases + (replace 'bootstrap + ;; The bootstrap script is missing a shebang. + (lambda _ + (invoke "bash" "./bootstrap.sh"))) (add-after 'unpack 'fix-includes (lambda _ (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp" "src/mash/CommandScreen.cpp") (("^#include \"kseq\\.h\"") - "#include \"htslib/kseq.h\"")) - #t)) + "#include \"htslib/kseq.h\"")))) (add-after 'fix-includes 'use-c++14 (lambda _ - ;; capnproto 0.7 requires c++14 to build - (substitute* "configure.ac" - (("c\\+\\+11") "c++14")) - (substitute* "Makefile.in" - (("c\\+\\+11") "c++14")) - #t))))) + ;; capnproto 1.0 requires c++14 to build. + (substitute* (list "configure.ac" "Makefile.in") + (("c\\+\\+11") "c++14"))))))) (native-inputs (list autoconf)) (inputs @@ -8325,7 +8432,7 @@ accessed/downloaded on demand across HTTP.") (inputs (list zlib lapack)) (native-inputs - (list unzip)) + (list unzip gcc-8)) (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") (synopsis "Whole genome association analysis toolset") (description @@ -14950,11 +15057,11 @@ activity prediction from transcriptomics data, and its R implementation (license license:expat)))) (define-public r-liana - (let ((commit "efb1249af46f576d1d620956053cfa93b2cee961") + (let ((commit "10d81773e0874de676eb106ce56e3cf9d4fe01d3") (revision "1")) (package (name "r-liana") - (version (git-version "0.1.5" revision commit)) + (version (git-version "0.1.11" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -14963,13 +15070,13 @@ activity prediction from transcriptomics data, and its R implementation (file-name (git-file-name name version)) (sha256 (base32 - "0z645k26kqrfj5f1s412vwclw1q47h1zfxxrh9ijr30pxhpv6cv0")))) + "0b0m8i9kava36s3cn6vnn5vmiwvqwxmcq8jacy6ccshsji3kgp09")))) (properties `((upstream-name . "liana"))) (build-system r-build-system) (arguments (list #:phases - `(modify-phases %standard-phases + '(modify-phases %standard-phases ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) |