Revert "gnu: Add freebayes."

This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.

1 files changed, 0 insertions, 123 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 311a83e53b..7808976a1f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15100,126 +15100,3 @@ 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 freebayes
-  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
-        (revision "1")
-        (version "1.0.2"))
-    (package
-      (name "freebayes")
-      (version (git-version version revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/ekg/freebayes.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
-      (build-system gnu-build-system)
-      (inputs
-       `(("zlib" ,zlib)
-         ("htslib" ,htslib)))
-      (native-inputs
-       `(("bc" ,bc)                     ; Needed for running tests.
-         ("samtools" ,samtools)         ; Needed for running tests.
-         ("parallel" ,parallel)         ; Needed for running tests.
-         ("perl" ,perl)                 ; Needed for running tests.
-         ("procps" ,procps)             ; Needed for running tests.
-         ("python" ,python-2)           ; Needed for running tests.
-         ("bamtools" ,bamtools)
-         ("vcflib-src" ,(package-source vcflib))
-         ;; These are submodules for the vcflib version used in freebayes.
-         ;; This package builds against the .o files so we need to extract the source.
-         ("tabixpp-src" ,(package-source tabixpp-freebayes))
-         ("smithwaterman-src" ,(package-source smithwaterman))
-         ("multichoose-src" ,(package-source multichoose))
-         ("fsom-src" ,(package-source fsom))
-         ("filevercmp-src" ,(package-source filevercmp))
-         ("fastahack-src" ,(package-source fastahack))
-         ("intervaltree-src"
-          ,(origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/ekg/intervaltree/")
-                   (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
-             (file-name "intervaltree-src-checkout")
-             (sha256
-              (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
-         ;; These submodules are needed to run the tests.
-         ("bash-tap-src" ,(package-source bash-tap))
-         ("test-simple-bash-src"
-          ,(origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/ingydotnet/test-simple-bash/")
-                   (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
-             (file-name "test-simple-bash-src-checkout")
-             (sha256
-              (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
-      (arguments
-       `(#:tests? #f    ; TODO: Re-enable when we have grep with perl support.
-         #:test-target "test"
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (add-after 'unpack 'unpack-submodule-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((unpack (lambda (source target)
-                               (with-directory-excursion target
-                                 (if (file-is-directory? (assoc-ref inputs source))
-                                     (copy-recursively (assoc-ref inputs source) ".")
-                                     (invoke "tar" "xvf"
-                                             (assoc-ref inputs source)
-                                             "--strip-components=1"))))))
-                 (and
-                  (unpack "vcflib-src" "vcflib")
-                  (unpack "fastahack-src" "vcflib/fastahack")
-                  (unpack "filevercmp-src" "vcflib/filevercmp")
-                  (unpack "fsom-src" "vcflib/fsom")
-                  (unpack "intervaltree-src" "vcflib/intervaltree")
-                  (unpack "multichoose-src" "vcflib/multichoose")
-                  (unpack "smithwaterman-src" "vcflib/smithwaterman")
-                  (unpack "tabixpp-src" "vcflib/tabixpp")
-                  (unpack "test-simple-bash-src" "test/test-simple-bash")
-                  (unpack "bash-tap-src" "test/bash-tap")))))
-           (add-after 'unpack-submodule-sources 'fix-makefile
-             (lambda* (#:key inputs #:allow-other-keys)
-               ;; We don't have the .git folder to get the version tag from.
-               (substitute* '("vcflib/Makefile")
-                 (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version)))))
-           (replace 'build
-             (lambda* (#:key inputs make-flags #:allow-other-keys)
-               (with-directory-excursion "vcflib"
-                 (with-directory-excursion "tabixpp"
-                   (pk "Compile tabixpp before compiling the main project.")
-                   (let ((htslib-ref (assoc-ref inputs "htslib")))
-                     (invoke "make" "HTS_HEADERS="
-                             (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
-                             (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))
-                 (pk "Compile vcflib before compiling the main project.")
-                 (invoke "make" "CC=gcc"
-                         (string-append "CFLAGS=\"" "-Itabixpp "
-                                        "-I" (assoc-ref inputs "htslib") "/include " "\"")
-                         "all"))
-               (pk "Compile the main project.")
-               (with-directory-excursion "src"
-                 (substitute* "Makefile"
-                   (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
-                 (invoke "make"
-                         (string-append "BAMTOOLS_ROOT="
-                                        (assoc-ref inputs "bamtools"))))))
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "bin/freebayes" bin)
-                 (install-file "bin/bamleftalign" bin))
-               #t)))))
-      (home-page "https://github.com/ekg/freebayes")
-      (synopsis "Haplotype-based variant detector")
-      (description "FreeBayes is a Bayesian genetic variant detector designed to
-find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
-indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
-complex events (composite insertion and substitution events) smaller than the
-length of a short-read sequencing alignment.")
-      (license license:expat))))