diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 160 |
1 files changed, 121 insertions, 39 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 26fcc3a41a..9b0a4314b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1752,6 +1752,72 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public python2-plastid (package-with-python2 python-plastid)) +(define-public tetoolkit + (package + (name "tetoolkit") + (version "2.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mhammell-laboratory/tetoolkit.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; not guaranteed to work with Python 3 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-writable + (lambda _ + (for-each make-file-writable (find-files ".")) + #t)) + (add-after 'unpack 'patch-invocations + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("bin/TEtranscripts" + "bin/TEcount") + (("'sort ") + (string-append "'" (which "sort") " ")) + (("'rm -f ") + (string-append "'" (which "rm") " -f ")) + (("'Rscript'") (string-append "'" (which "Rscript") "'"))) + (substitute* "TEToolkit/IO/ReadInputs.py" + (("BamToBED") (which "bamToBed"))) + (substitute* "TEToolkit/Normalization.py" + (("\"Rscript\"") + (string-append "\"" (which "Rscript") "\""))) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure the executables find R packages. + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (script) + (wrap-program (string-append out "/bin/" script) + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + '("TEtranscripts" + "TEcount"))) + #t))))) + (inputs + `(("coreutils" ,coreutils) + ("bedtools" ,bedtools) + ("python-argparse" ,python2-argparse) + ("python-pysam" ,python2-pysam) + ("r-minimal" ,r-minimal) + ("r-deseq2" ,r-deseq2))) + (home-page "https://github.com/mhammell-laboratory/tetoolkit") + (synopsis "Transposable elements in differential enrichment analysis") + (description + "This is package for including transposable elements in differential +enrichment analysis of sequencing datasets. TEtranscripts and TEcount take +RNA-seq (and similar data) and annotates reads to both genes and transposable +elements. TEtranscripts then performs differential analysis using DESeq2. +Note that TEtranscripts and TEcount rely on specially curated GTF files, which +are not included due to their size.") + (license license:gpl3+))) + (define-public cd-hit (package (name "cd-hit") @@ -10293,35 +10359,6 @@ quality controls, normalization, visualization, and further analysis are also provided.") (license license:artistic2.0))) -(define-public r-qvalue - (package - (name "r-qvalue") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "qvalue" version)) - (sha256 - (base32 - "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) - (home-page "http://github.com/jdstorey/qvalue") - (synopsis "Q-value estimation for false discovery rate control") - (description - "This package takes a list of p-values resulting from the simultaneous -testing of many hypotheses and estimates their q-values and local @dfn{false -discovery rate} (FDR) values. The q-value of a test measures the proportion -of false positives incurred when that particular test is called significant. -The local FDR measures the posterior probability the null hypothesis is true -given the test's p-value. Various plots are automatically generated, allowing -one to make sensible significance cut-offs. The software can be applied to -problems in genomics, brain imaging, astrophysics, and data mining.") - ;; Any version of the LGPL. - (license license:lgpl3+))) - (define-public r-hdf5array (package (name "r-hdf5array") @@ -11908,21 +11945,35 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "loompy" version)) - (sha256 - (base32 - "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) + (version "2.0.17") + ;; The tarball on Pypi does not include the tests. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linnarsson-lab/loompy.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) (build-system python-build-system) - ;; There are no tests - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "PYTHONPATH"))) + (invoke "pytest" "tests") + #t))))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -14158,3 +14209,34 @@ short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.") (license license:gpl2+))) + +(define-public python-velocyto + (package + (name "python-velocyto") + (version "0.17.17") + (source + (origin + (method url-fetch) + (uri (pypi-uri "velocyto" version)) + (sha256 + (base32 + "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs")))) + (build-system python-build-system) + (propagated-inputs + `(("python-click" ,python-click) + ("python-cython" ,python-cython) + ("python-h5py" ,python-h5py) + ("python-loompy" ,python-loompy) + ("python-matplotlib" ,python-matplotlib) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/velocyto-team/velocyto.py") + (synopsis "RNA velocity analysis for single cell RNA-seq data") + (description + "Velocyto is a library for the analysis of RNA velocity. Velocyto +includes a command line tool and an analysis pipeline.") + (license license:bsd-2))) |