Removed (delly)

1 files changed, 0 insertions, 56 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 0b6521e..af7724d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -95,20 +95,6 @@
   #:use-module (gnu packages zig)
   #:use-module (past packages python27))
 
-(define boost-delly
-  (package (inherit boost)
-    (name "boost-delly")
-    (version "1.57.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "mirror://sourceforge/boost/boost_"
-                    (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
-                    ".tar.bz2"))
-              (sha256
-               (base32
-                "0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))
-
 (define-public verkko
   (let ((commit "9323e71f46b0ea1725202ebe911142d0d1288c45")     ; Jan 22, 2022
         (revision "1"))
@@ -756,48 +742,6 @@ annotated in the reference.")
     (description "A dendrogram object in R are is a list structure with attributes in its nodes and leaves.")
     (license license:gpl3)))
 
-(define-public delly
-  (package
-    (name "delly")
-    (version "0.7.2")
-    (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
-            version ".tar.gz"))
-      (sha256
-       (base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
-      (patches (list (search-patch "delly-use-system-libraries.patch")))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(("python" ,python-2)))
-    (inputs
-     `(("boost" ,boost-delly) ; Use version 1.57.0 instead.
-       ("htslib" ,htslib)
-       ("zlib" ,zlib)
-       ("bzip2" ,bzip2)))
-    (arguments
-     `(#:tests? #f ; There are no tests to run.
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure) ; There is no configure phase.
-         (replace 'install
-           (lambda _
-             (let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
-               (install-file "src/cov" bin)
-               (install-file "src/delly" bin)
-               (install-file "src/extract" bin)
-               (install-file "src/iover" bin)
-               (install-file "src/stats" bin)))))))
-    (home-page "https://github.com/tobiasrausch/delly")
-    (synopsis "Integrated structural variant prediction method")
-    (description "Delly is an integrated structural variant prediction method
-that can discover and genotype deletions, tandem duplications, inversions and
-translocations at single-nucleotide resolution in short-read massively parallel
-sequencing data.  It uses paired-ends and split-reads to sensitively and
-accurately delineate genomic rearrangements throughout the genome.  Structural
-variants can be visualized using Delly-maze and Delly-suave.")
-    (license license:gpl3)))
-
 (define-public plink-ng-gn
   (let ((commit "5d1db4313ba0cc976562da233db4aced78975d10"))
   (package