gn: Remove some upstreamed packages

1 files changed, 0 insertions, 480 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 040373c..00eab03 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -222,486 +222,6 @@ data.  For whole genome sequencing data analysis, the program can also use
 mappability data (files created by GEM). ")
     (license license:gpl2+)))
 
-(define-public tabixpp
-  (package
-   (name "tabixpp")
-   (version "1.0.0")
-   (source (origin
-     (method url-fetch)
-     (uri (string-append "https://github.com/ekg/tabixpp/archive/v"
-                         version ".tar.gz"))
-     (file-name (string-append name "-" version ".tar.gz"))
-     (sha256
-      (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn"))))
-   (build-system gnu-build-system)
-   (inputs
-    `(("htslib" ,htslib)
-      ("zlib" ,zlib)))
-   (arguments
-    `(#:tests? #f ; There are no tests to run.
-      #:phases
-      (modify-phases %standard-phases
-        (delete 'configure) ; There is no configure phase.
-        ;; The build phase needs overriding the location of htslib.
-        (replace 'build
-          (lambda* (#:key inputs #:allow-other-keys)
-            (let ((htslib-ref (assoc-ref inputs "htslib")))
-              (zero?
-               (system* "make"
-                 (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
-                 "HTS_HEADERS=" ; No need to check for headers here.
-                 (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))))
-        (replace 'install
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-              (install-file "tabix++" bin)))))))
-   (home-page "https://github.com/ekg/tabixpp")
-   (synopsis "C++ wrapper around tabix project")
-   (description "This is a C++ wrapper around the Tabix project which abstracts
-some of the details of opening and jumping in tabix-indexed files.")
-   (license license:expat)))
-
-;; This version works with FreeBayes while the released version doesn't. The
-;; released creates a variable with the name "vcf" somewhere, which is also the
-;; name of a namespace in vcflib.
-(define-public tabixpp-freebayes
-  (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
-    (package (inherit tabixpp)
-      (name "tabixpp-freebayes")
-      (version (string-append "0-1." (string-take commit 7)))
-      (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/tabixpp/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version "-checkout.tar.gz"))
-        (sha256
-         (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))))))
-
-(define-public smithwaterman
-  ;; TODO: Upgrading smithwaterman breaks FreeBayes.
-  (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
-    (package
-      (name "smithwaterman")
-      (version (string-append "0-1." (string-take commit 7)))
-      (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version "-checkout.tar.gz"))
-        (sha256
-         (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "smithwaterman" bin)))))))
-      (home-page "https://github.com/ekg/smithwaterman")
-      (synopsis "Implementation of the Smith-Waterman algorithm")
-      (description "Implementation of the Smith-Waterman algorithm.")
-      ;; The project contains a license file for the GPLv2.  The source files
-      ;; do not contain a license notice, so GPLv2-only is assumed here.
-      (license license:gpl2))))
-
-(define-public multichoose
-  (package
-    (name "multichoose")
-    (version "1.0.3")
-    (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/ekg/multichoose/archive/v"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
-      (sha256
-       (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l"))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(("python" ,python-2)
-       ("node" ,node)))
-    (arguments
-     `(#:tests? #f ; There are no tests to run.
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure) ; There is no configure phase.
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-               ;; TODO: There are Python modules for these programs too.
-               (install-file "multichoose" bin)
-               (install-file "multipermute" bin)))))))
-    (home-page "https://github.com/ekg/multichoose")
-    (synopsis "Library for efficient loopless multiset combination generation
-algorithm")
-    (description "A library implements an efficient loopless multiset
-combination generation algorithm which is (approximately) described in
-\"Loopless algorithms for generating permutations, combinations, and other
-combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
-1973. (Algorithm 7.)")
-    (license license:expat)))
-
-(define-public fsom
-  (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
-    (package
-      (name "fsom")
-      (version (string-append "0-1." (string-take commit 7)))
-      (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/fsom/archive/"
-                            "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
-        (file-name (string-append name "-" version "-checkout.tar.gz"))
-        (sha256
-         (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "fsom" bin)))))))
-      (home-page "https://github.com/ekg/fsom")
-      (synopsis "Program for managing SOM (Self-Organizing Maps) neural networks")
-      (description "Program for managing SOM (Self-Organizing Maps) neural networks.")
-      (license license:gpl3))))
-
-(define-public filevercmp
-  (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
-    (package
-      (name "filevercmp")
-      (version (string-append "0-1." (string-take commit 7)))
-      (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                            commit ".tar.gz"))
-        (file-name "filevercmp-src.tar.gz")
-        (sha256
-         (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "filevercmp" bin)))))))
-      (home-page "https://github.com/ekg/filevercmp")
-      (synopsis "Program to compare version strings")
-      (description "A program to compare version strings.  It intends to be a
-replacement for strverscmp.")
-      (license license:gpl3+))))
-
-(define-public fastahack ; guix ready
-  (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
-    (package
-      (name "fastahack")
-      (version (string-append "0-1." (string-take commit 7)))
-      (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/fastahack/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version "-checkout.tar.gz"))
-        (sha256
-         (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "fastahack" bin)))))))
-      (home-page "https://github.com/ekg/fastahack")
-      (synopsis "Program for indexing and sequence extraction from FASTA files")
-      (description "Fastahack is a small application for indexing and extracting
-sequences and subsequences from FASTA files.  The included Fasta.cpp library
-provides a FASTA reader and indexer that can be embeddedinto applications which
-would benefit from directly reading subsequences from FASTA files.  The library
-automatically handles index file generation and use.")
-      ;; There is no specific license for fastahack.
-      ;; A part of the program is licensed GPLv2.
-      (license (list license:non-copyleft license:gpl2)))))
-
-(define-public vcflib
-  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
-    (package
-      (name "vcflib")
-      (version (string-append "1.0.2-1." (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)
-         ("r" ,r)
-         ("node" ,node)
-         ("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 url-fetch)
-             (uri (string-append
-                   "https://github.com/ekg/intervaltree/archive/"
-                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
-             (file-name "intervaltree-src.tar.gz")
-             (sha256
-              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))))
-      (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 "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"))
-                    ;;(include (string-append (assoc-ref outputs "out") "/include"))
-                    (lib (string-append (assoc-ref outputs "out") "/lib")))
-                (for-each (lambda (file)
-                           (install-file file bin))
-                         (find-files "bin" ".*"))
-                ;; The header files do not correspond to libvcflib.a, therefore
-                ;; I left them out.
-                ;;(for-each (lambda (file)
-                ;;           (install-file file include))
-                ;;         (find-files "src" "\\.h$"))
-                (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 bash-tap ; guix license issue
-  (package
-    (name "bash-tap")
-    (version "1.0.2")
-    (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/illusori/bash-tap/archive/"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
-      (sha256
-       (base32 "0qs1qi38bl3ns4mpagcawv618dsk2q1lgrbddgvs0wl3ia12cyz5"))))
-    (build-system trivial-build-system)
-    (native-inputs `(("source" ,source)
-                     ("tar" ,tar)
-                     ("gzip" ,gzip)))
-    (arguments
-     `(#:modules ((guix build utils))
-       #:builder (begin
-                   (use-modules (guix build utils))
-                   (let ((tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
-                         (path (string-append (assoc-ref %build-inputs "gzip") "/bin"))
-                         (bin (string-append %output "/bin"))
-                         (source (string-append (assoc-ref %build-inputs "source"))))
-                     (setenv "PATH" path)
-                     (mkdir-p bin)
-                     (with-directory-excursion bin
-                       (zero? (system* tar "xvf" source
-                                       "--strip-components=1"
-                                       "--no-anchored"
-                                       "bash-tap"
-                                       "bash-tap-bootstrap"
-                                       "bash-tap-mock")))))))
-    (home-page "http://www.illusori.co.uk/projects/bash-tap/")
-    (synopsis "Bash port of a Test::More/Test::Builder-style TAP-compliant
-test library")
-    (description "Bash TAP is a TAP-compliant Test::More-style testing library
-for Bash shell scripts and functions.  Along with the Test::More-style testing
-helpers it provides helper functions for mocking commands and functions and
-in-process output capturing.")
-    ;; The author didn't specify a license.
-    (license license:public-domain)))
-
-(define-public freebayes ; guix dependent package issues
-  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
-        (revision "1"))
-    (package
-      (name "freebayes")
-      (version (string-append "1.0.2-" revision "." (string-take commit 7)))
-      (source (origin
-        (method git-fetch)
-        (uri (git-reference
-          (url "https://github.com/ekg/freebayes.git")
-          (commit commit)))
-        (file-name (string-append name "-" version "-checkout"))
-        (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.
-         ("procps" ,procps) ; Needed for running tests.
-         ("bamtools" ,bamtools)
-         ("cmake" ,cmake)
-         ("python" ,python-2)
-         ("node" ,node)
-         ("r" ,r)
-         ("perl" ,perl)
-         ("bamtools-src" ,(package-source bamtools))
-         ("vcflib-src" ,(package-source vcflib))
-         ;; These are submodules for the vcflib version used in freebayes
-         ("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 url-fetch)
-             (uri (string-append
-                   "https://github.com/ekg/intervaltree/archive/"
-                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
-             (file-name "intervaltree-src.tar.gz")
-             (sha256
-              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
-         ;; These submodules are needed to run the tests.
-         ("bash-tap-src" ,(package-source bash-tap))
-          ;; ,(origin
-          ;;   (method url-fetch)
-          ;;   (uri (string-append "https://github.com/illusori/bash-tap/archive/"
-          ;;                       "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz"))
-          ;;   (file-name "bash-tap-src.tar.gz")
-          ;;   (sha256
-          ;;    (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz"))))
-         ("test-simple-bash-src"
-          ,(origin
-            (method url-fetch)
-            (uri (string-append "https://github.com/ingydotnet/test-simple-bash/archive/"
-                                "124673ff204b01c8e96b7fc9f9b32ee35d898acc" ".tar.gz"))
-            (file-name "test-simple-bash-src.tar.gz")
-            (sha256
-             (base32 "016xf3wbgqbav9dncvfdx5k0f10z5xwq8jdszajzmcvnhz5wis14"))))))
-      (arguments
-       `(#: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
-                                 (zero? (system* "tar" "xvf"
-                                                 (assoc-ref inputs source)
-                                                 "--strip-components=1"))))))
-                 (and
-                  (unpack "bamtools-src" "bamtools")
-                  (unpack "vcflib-src" "vcflib")
-                  ;;(unpack "intervaltree-src" "intervaltree")
-                  (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.
-               ;; For this checkout of the code, it's v1.0.0.
-               (substitute* '("vcflib/Makefile")
-                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
-           (replace 'build
-            (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (and
-               ;; Compile Bamtools before compiling the main project.
-               (with-directory-excursion "bamtools"
-                 (system* "mkdir" "build")
-                 (with-directory-excursion "build"
-                   (and (zero? (system* "cmake" "../"))
-                        (zero? (system* "make")))))
-               ;; Compile vcflib before we compiling the main project.
-               (with-directory-excursion "vcflib"
-                 (with-directory-excursion "tabixpp"
-                   (let ((htslib-ref (assoc-ref inputs "htslib")))
-                     (zero?
-                      (system* "make" "HTS_HEADERS="
-                               (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
-                               (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
-                 (zero? (system* "make" "CC=gcc"
-                   (string-append "CFLAGS=\"" "-Itabixpp "
-                     "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
-               (with-directory-excursion "src"
-                 (zero? (system* "make"))))))
-           (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))))
-           ;; There are three tests that fail.  All because of the -P
-           ;; (--perl-regexp) option in grep, which is not compiled into the
-           ;; version of grep in Guix.
-           (replace 'check
-            (lambda* (#:key inputs #:allow-other-keys)
-              (system* "make" "test"))))))
-      (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))))
-
 (define-public plink2
   (package
     (name "plink2")