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01/06: gnu: Add r-flames.
From: |
guix-commits |
Subject: |
01/06: gnu: Add r-flames. |
Date: |
Fri, 19 Jan 2024 18:34:15 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit d8c718d44c8d402e49982658c045bfb6dbb2c030
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Jan 19 14:58:34 2024 +0100
gnu: Add r-flames.
* gnu/packages/bioconductor.scm (r-flames): New variable.
Change-Id: I551a8f9d7de16e2281898b9541572dd244aadc36
---
gnu/packages/bioconductor.scm | 72 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90ca2ae52a..5e7dcfd1f2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17657,6 +17657,78 @@ gene fusion discovery. It can be applied to all major
sequencing techologies
and to both short and long sequence reads.")
(license license:gpl3)))
+(define-public r-flames
+ (package
+ (name "r-flames")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FLAMES" version))
+ (sha256
+ (base32 "0937zag0h4bvpapld267s5gz36h8zgjrgvbng9m7czdd8w6064ns"))))
+ (properties `((upstream-name . "FLAMES")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'fix-build-system
+ (lambda _
+ ;; One target uses & instead of &&, which leads to a command
+ ;; being run despite the check failing.
+ (substitute* "src/Makevars"
+ ((" & ") " && ")))))))
+ (propagated-inputs
+ (list r-bambu
+ r-basilisk
+ r-biocgenerics
+ r-biostrings
+ r-circlize
+ r-complexheatmap
+ r-cowplot
+ r-dplyr
+ r-dropletutils
+ r-future
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggbio
+ r-ggplot2
+ r-gridextra
+ r-igraph
+ r-jsonlite
+ r-magrittr
+ r-matrix
+ r-multiassayexperiment
+ r-rcolorbrewer
+ r-rcpp
+ r-reticulate
+ r-rhtslib
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-scater
+ r-scran
+ r-scuttle
+ r-singlecellexperiment
+ r-stringr
+ r-summarizedexperiment
+ r-tidyr
+ r-withr
+ r-zlibbioc))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/OliverVoogd/FLAMES")
+ (synopsis
+ "Full Length Analysis of Mutations and Splicing in long read RNA-seq
data")
+ (description
+ "This is a package for semi-supervised isoform detection and annotation
+from both bulk and single-cell long read RNA-seq data. Flames provides
+automated pipelines for analysing isoforms, as well as intermediate functions
+for manual execution.")
+ (license license:gpl2+)))
+
(define-public r-flowai
(package
(name "r-flowai")
- branch master updated (f7c0ccb186 -> eb1d80ac77), guix-commits, 2024/01/19
- 01/06: gnu: Add r-flames.,
guix-commits <=
- 04/06: gnu: Add r-modstrings., guix-commits, 2024/01/19
- 06/06: gnu: Add r-trnadbimport., guix-commits, 2024/01/19
- 05/06: gnu: Add r-trna., guix-commits, 2024/01/19
- 02/06: gnu: Add python-mediapy., guix-commits, 2024/01/19
- 03/06: gnu: Add r-structstrings., guix-commits, 2024/01/19