diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4cf6900498..8a49e1e350 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8290,6 +8290,9 @@ secondary structure and comparative analysis in R.") "13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) + ;; Without this a temporary directory ends up in the Rhtslib.so binary, + ;; which makes R abort the build. + (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) (inputs @@ -9953,6 +9956,16 @@ effort and encourages consistency.") (base32 "0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationfilter" ,r-annotationfilter) @@ -14739,3 +14752,38 @@ tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.") (license license:gpl3+))) + +(define-public umi-tools + (package + (name "umi-tools") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "umi_tools" version)) + (sha256 + (base32 + "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools) + ("python-pandas" ,python-pandas) + ("python-future" ,python-future) + ("python-scipy" ,python-scipy) + ("python-matplotlib" ,python-matplotlib) + ("python-regex" ,python-regex) + ("python-pysam" ,python-pysam))) + (native-inputs + `(("python-setuptools" ,python-setuptools) + ("python-cython" ,python-cython))) + (home-page "https://github.com/CGATOxford/UMI-tools") + (synopsis "Tools for analyzing unique modular identifiers") + (description "This package provides tools for dealing with @dfn{Unique +Molecular Identifiers} (UMIs) and @dfn{Random Molecular Tags} (RMTs) in +genetic sequences. There are six tools: the @code{extract} and +@code{whitelist} commands are used to prepare a fastq containg UMIs @code{+/-} +cell barcodes for alignment. The remaining commands, @code{group}, +@code{dedup}, and @{count}/@code{count_tab}, are used to identify PCR +duplicates using the UMIs and perform different levels of analysis depending +on the needs of the user.") + (license license:expat))) |