diff mbox series

[bug#48575,24/50] gnu: r-gage: Move to (gnu packages bioconductor).

Message ID 20210521202622.26591-24-zimon.toutoune@gmail.com
State Accepted
Headers show
Series Move some Bioconductor packages to (gnu packages bioconductor). | expand

Checks

Context Check Description
cbaines/comparison success View comparision
cbaines/git branch success View Git branch
cbaines/applying patch success View Laminar job
cbaines/issue success View issue

Commit Message

zimoun May 21, 2021, 8:25 p.m. UTC
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)
diff mbox series

Patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ee670e858..f6d3ef897a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@ 
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
@@ -2294,6 +2294,37 @@  formats can be used as input to fastseg like expression set objects for
 microarrays or GRanges for sequencing data.")
     (license license:lgpl2.0+)))
 
+(define-public r-gage
+  (package
+    (name "r-gage")
+    (version "2.40.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gage" version))
+       (sha256
+        (base32
+         "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-keggrest" ,r-keggrest)))
+    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+                              "articles/10.1186/1471-2105-10-161"))
+    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+    (description
+     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity.  The gage package provides functions for
+basic GAGE analysis, result processing and presentation.  In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms.  These functions and data are also useful for gene set
+analysis using other methods.")
+    (license license:gpl2+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dacf8a342..daf1fb6958 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,37 +8994,6 @@  their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-gage
-  (package
-    (name "r-gage")
-    (version "2.40.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gage" version))
-       (sha256
-        (base32
-         "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-keggrest" ,r-keggrest)))
-    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
-                              "articles/10.1186/1471-2105-10-161"))
-    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
-    (description
-     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
-analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
-data attributes including sample sizes, experimental designs, assay platforms,
-and other types of heterogeneity.  The gage package provides functions for
-basic GAGE analysis, result processing and presentation.  In addition, it
-provides demo microarray data and commonly used gene set data based on KEGG
-pathways and GO terms.  These functions and data are also useful for gene set
-analysis using other methods.")
-    (license license:gpl2+)))
-
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")