gn: Remove some duplicate packages

1 files changed, 1 insertions, 130 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5ee126e..e5914c2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -431,7 +431,7 @@ automatically handles index file generation and use.")
       ;; A part of the program is licensed GPLv2.
       (license (list license:non-copyleft license:gpl2)))))
 
-(define-public vcflib ; guix duplicat, see below?
+(define-public vcflib
   (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
     (package
       (name "vcflib")
@@ -808,135 +808,6 @@ integration with gPLINK and Haploview, there is some support for the
 subsequent visualization, annotation and storage of results.")
     (license license:gpl3+))))
 
-
-(define-public vcflib ; duplicate? See above
-  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
-    (package
-      (name "vcflib")
-      (version (string-append "v1.0.2-" (string-take commit 7)))
-      (source
-       (origin
-         (method url-fetch)
-         (uri (string-append "https://github.com/vcflib/vcflib/archive/"
-                "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
-         (file-name "vcflib-5ac0913.tar.gz")
-         (sha256
-          (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
-      (build-system gnu-build-system)
-      (native-inputs
-       `(("htslib" ,htslib)
-         ("zlib" ,zlib)
-         ("python" ,python-2)
-         ("perl" ,perl)
-         ("tabixpp-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/tabixpp/archive/"
-                  "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
-            (file-name "tabixpp-src.tar.gz")
-            (sha256
-             (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
-         ("intervaltree-src"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://github.com/ekg/intervaltree/archive/"
-                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
-             (file-name "intervaltree-src.tar.gz")
-             (sha256
-              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
-         ("smithwaterman-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
-                  "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
-            (file-name "smithwaterman-src.tar.gz")
-            (sha256
-             (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
-         ("multichoose-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/multichoose/archive/"
-                  "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
-            (file-name "multichoose-src.tar.gz")
-            (sha256
-             (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
-         ("fsom-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/fsom/archive/"
-                  "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
-            (file-name "fsom-src.tar.gz")
-            (sha256
-             (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
-         ("filevercmp-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                  "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
-            (file-name "filevercmp-src.tar.gz")
-            (sha256
-             (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
-         ("fastahack-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ekg/fastahack/archive/"
-                  "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
-            (file-name "fastahack-src.tar.gz")
-            (sha256
-             (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))))
-      (arguments
-       `(#:tests? #f
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (delete 'check)
-           (add-after 'unpack 'unpack-submodule-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((unpack (lambda (source target)
-                               (with-directory-excursion target
-                                 (zero? (system* "tar" "xvf"
-                                        (assoc-ref inputs source)
-                                        "--strip-components=1"))))))
-                 (and
-                  (unpack "intervaltree-src" "intervaltree")
-                  (unpack "fastahack-src" "fastahack")
-                  (unpack "filevercmp-src" "filevercmp")
-                  (unpack "fsom-src" "fsom")
-                  (unpack "intervaltree-src" "intervaltree")
-                  (unpack "multichoose-src" "multichoose")
-                  (unpack "smithwaterman-src" "smithwaterman")
-                  (unpack "tabixpp-src" "tabixpp")))))
-           (add-after 'unpack-submodule-sources 'fix-makefile
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* '("Makefile")
-                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
-           (replace
-            'build
-            (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (with-directory-excursion "tabixpp"
-                (zero? (system* "make")))
-              (zero? (system* "make" "CC=gcc"
-                (string-append "CFLAGS=\"" "-Itabixpp "
-                  "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))))
-           (replace
-            'install
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                    (lib (string-append (assoc-ref outputs "out") "/lib")))
-                (for-each (lambda (file)
-                           (install-file file bin))
-                         (find-files "bin" ".*"))
-                (install-file "libvcflib.a" lib)))))))
-      (home-page "https://github.com/vcflib/vcflib/")
-      (synopsis "Library for parsing and manipulating VCF files")
-      (description "Vcflib provides methods to manipulate and interpret
-sequence variation as it can be described by VCF. It is both an API for parsing
-and operating on records of genomic variation as it can be described by the VCF
-format, and a collection of command-line utilities for executing complex
-manipulations on VCF files.")
-      (license license:expat))))
-
 (define-public pindel
   (package
    (name "pindel")