Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

1 files changed, 266 insertions, 707 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index bdd0322..ad4db7b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -7,60 +7,20 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system ant)
-  #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
-  #:use-module (guix build-system perl)
+  #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
-  ;; #:use-module (guix build-system ruby)
-  #:use-module (guix build-system r)
-  #:use-module (guix build-system trivial)
-  #:use-module (gn packages statistics)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages base)
+  #:use-module (gnu packages)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages databases)
   #:use-module (gnu packages check)
-  #:use-module (gnu packages cmake)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpio)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages documentation)
-  #:use-module (gnu packages datastructures)
-  #:use-module (gnu packages file)
-  #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
-  #:use-module (gnu packages graphviz)
-  #:use-module (gnu packages java)
-  #:use-module (gnu packages linux)
-  #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages node)
-  #:use-module (gnu packages parallel)
-  #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages popt)
-  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages ruby)
-  #:use-module (gnu packages statistics)
-  #:use-module (gnu packages tbb)
-  #:use-module (gnu packages textutils)
-  #:use-module (gnu packages time)
-  #:use-module (gnu packages tls)
-  #:use-module (gnu packages vim)
-  #:use-module (gnu packages web)
-  #:use-module (gnu packages xml)
-  #:use-module (gnu packages bootstrap)
-  #:use-module (gnu packages dlang)
-;  #:use-module (gn packages ldc)
-  #:use-module (gn packages shell)
-  #:use-module (srfi srfi-1))
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages statistics))
 
 (define-public contra
   (package
@@ -69,10 +29,15 @@
     (source (origin
       (method url-fetch)
       (uri (string-append
-            "mirror://sourceforge/contra-cnv/CONTRA.v" version ".tar.gz"))
+            "mirror://sourceforge/contra-cnv/CONTRA.V"
+            (version-major+minor version) "/CONTRA.v" version ".tar.gz"))
       (sha256
        (base32
-        "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))))
+        "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))
+      (modules '((guix build utils)))
+      (snippet
+       '(begin
+          (delete-file "BEDTools.v2.11.2.tar.gz") #t))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("python" ,python-2)
@@ -87,18 +52,16 @@
          (delete 'configure)
          (delete 'build) ; We can use Guix's BEDtools instead.
          (replace 'install
-           (lambda _
-             (let* ((out (assoc-ref %outputs "out"))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
                     (doc (string-append out "/share/doc/contra")))
-               (mkdir-p bin)
-               (mkdir-p doc)
-               (and
-                (zero? (system* "cp" "--recursive" "scripts" bin))
-                (zero? (system* "cp" "contra.py" bin))
-                (zero? (system* "cp" "baseline.py" bin))
-                ;; There's only a pre-built PDF available.
-                (zero? (system* "cp" "CONTRA_User_Guide.2.0.pdf" doc)))))))))
+               (copy-recursively "scripts" (string-append bin "/scripts"))
+               (install-file "contra.py" bin)
+               (install-file "baseline.py" bin)
+               ;; There's only a pre-built PDF available.
+               (install-file "CONTRA_User_Guide.2.0.pdf" doc))
+             #t)))))
     (home-page "http://contra-cnv.sourceforge.net/")
     (synopsis "Tool for copy number variation (CNV) detection for targeted
 resequencing data")
@@ -219,486 +182,6 @@ 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 ; guix duplicat, see below?
-  (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")
@@ -805,146 +288,18 @@ 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")
    (version "0.2.5b8")
    (source (origin
-     (method url-fetch)
-     (uri (string-append "https://github.com/genome/pindel/archive/v"
-                         version ".tar.gz"))
-     (file-name (string-append name "-" version ".tar.gz"))
+     (method git-fetch)
+     (uri (git-reference
+            (url "https://github.com/genome/pindel.git")
+            (commit (string-append "v" version))))
+     (file-name (git-file-name name version))
      (sha256
-      (base32 "06bsf0psxwf7h5p3j97xkh9k5qrwhxh6xn942y1j1m2inyhgs8bz"))))
+      (base32 "16a32fbgv1n58nfcxa1nyphrdrad80sgpinfa9p028n6plwycpww"))))
    (build-system gnu-build-system)
    (inputs
     `(("samtools" ,samtools)
@@ -968,7 +323,7 @@ manipulations on VCF files.")
             ;; The second run actually compiles the program.  Now Makefile.local
             ;; is available, and we should treat an exiting make with an error as
             ;; a true error.
-            (zero? (system* "make"))))
+            (invoke "make")))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
@@ -979,13 +334,11 @@ manipulations on VCF files.")
         ;; There are multiple test targets, so in order to run all
         ;; tests, we must run the separate make targets.
         (replace 'check
-          (lambda* (#:key inputs #:allow-other-keys)
-            (and
-             (zero? (system* "make" "acceptance-tests"))
-             (zero? (system* "make" "coverage-tests"))
-             (zero? (system* "make" "cppcheck"))
-             (zero? (system* "make" "functional-tests"))
-             (zero? (system* "make" "regression-tests"))))))))
+          (lambda _
+            (for-each (lambda (target)
+                        (invoke "make" target))
+                      '("acceptance-tests" "coverage-tests" "cppcheck"
+                        "functional-tests" "regression-tests")))))))
    (home-page "https://github.com/genome/pindel")
    (synopsis "Structural variants detector for next-gen sequencing data")
    (description "Pindel can detect breakpoints of large deletions, medium sized
@@ -1008,45 +361,251 @@ reads.")
        (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8"))))
     (build-system ant-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #f ; build.xml does not exist
+       #:phases
        (modify-phases %standard-phases
          (replace 'unpack
            (lambda _
              (mkdir "source")
              (chdir "source")
-             (and
-              ;; Unpack the Java archive containing the source files.
-              (zero? (system* "jar" "xf" (assoc-ref %build-inputs "source")))
-              ;; Remove existing compiled output.
-              (with-directory-excursion "net/sf/varscan/"
-                (for-each (lambda (file)
-                            (unless (string= (string-take-right file 5) ".java")
-                              (zero? (system* "rm" file))))
-                          (find-files "." #:directories? #f))))))
+             ;; Unpack the Java archive containing the source files.
+             (invoke "jar" "xf" (assoc-ref %build-inputs "source"))
+             ;; Remove existing compiled output.
+             (with-directory-excursion "net/sf/varscan/"
+               (for-each (lambda (file)
+                           (delete-file file))
+                         (find-files "." "^.java$" #:directories? #f)))
+             #t))
          (replace 'build
            (lambda _
-             (let ((classes '()))
-             (and
-              ;; Compile the source files.
-              (with-directory-excursion "net/sf/varscan/"
-                (for-each (lambda (file)
-                            (when (string= (string-take-right file 5) ".java")
-                              (zero? (system* "javac" file))
-                              (cons ))
-                          (find-files "." #:directories? #f)))
-              ;; Construct the new Java archive.
-              (zero? (system* "jar" "cfm" "varscan-2.4.1.jar"
-                              "META-INF/MANIFEST.MF"
-                              "net/sf/varscan/*.java")))))))
+             ;; Compile the source files.
+             (with-directory-excursion "net/sf/varscan/"
+               (for-each (lambda (file)
+                           (invoke "javac" file))
+                         (find-files "." ".java$" #:directories? #f)))
+             ;; Construct the new Java archive.
+             (apply invoke "jar" "cfm"
+                    (string-append "varscan-" ,version ".jar")
+                    "META-INF/MANIFEST.MF"
+                    (find-files "net/sf/varscan" ".java$"))))
         (replace 'install
-          (lambda _
-            (let ((out (string-append (assoc-ref %outputs "out")
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((out (string-append (assoc-ref outputs "out")
                                       "/share/java/varscan/")))
-              (mkdir-p out)
-              (install-file "varscan-2.4.1.jar" out)))))))
-    (home-page "http://dkoboldt.github.io/varscan/")
+              (install-file (string-append "varscan-" ,version ".jar") out))
+            #t)))))
+    (home-page "https://dkoboldt.github.io/varscan/")
     (synopsis "Variant detection in massively parallel sequencing data")
-    (description "")
+    (description "Variant detection in massively parallel sequencing data.")
     ;; Free for non-commercial use by academic, government, and
     ;; non-profit/not-for-profit institutions
     (license license:non-copyleft)))
+
+(define-public edirect-gn
+  (package
+    (inherit edirect)
+    (name "edirect-gn")
+    (arguments
+      (substitute-keyword-arguments (package-arguments edirect)
+        ((#:phases phases)
+         `(modify-phases ,phases
+         ;   (replace 'build
+         ;     (lambda* (#:key inputs #:allow-other-keys)
+         ;       (let ((go (string-append (assoc-ref inputs "go") "/bin/go")))
+         ;         (invoke go "build" "xtract.go"))))
+            (add-after 'unpack 'patch-programs
+              (lambda* (#:key inputs #:allow-other-keys)
+                (let ((gzip (assoc-ref inputs "gzip")))
+                  (substitute* '("index-bioc"
+                                 "pm-index"
+                                 "pm-invert"
+                                 "pm-stash"
+                                 "rchive.go"
+                                 "run-ncbi-converter")
+                    (("gunzip") (string-append gzip "/bin/gunzip")))
+                  (substitute* (find-files "." "^e")
+                    (("exec perl") "exec"))
+                  (substitute* '("xtract" "rchive")
+                    ;; or add current directory to PATH
+                    ((".*PATH.*") "")))
+                #t))
+            (replace 'install
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                      (xtract.linux (assoc-ref inputs "xtract.Linux"))
+                      (rchive.linux (assoc-ref inputs "rchive.Linux")))
+                  (for-each
+                    (lambda (file)
+                      (install-file file bin))
+                    '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed"
+                      "edirect.pl" "efetch" "epost" "fetch-pubmed" "ftp-cp"
+                      "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" "pm-stash"
+                      "rchive" "xtract"))
+                  (copy-file xtract.linux (string-append bin "/xtract.Linux"))
+                  (copy-file rchive.linux (string-append bin "/rchive.Linux"))
+                  (chmod (string-append bin "/xtract.Linux") #o555)
+                  (chmod (string-append bin "/rchive.Linux") #o555))
+                #t))
+            (replace 'wrap-program
+              (lambda* (#:key outputs #:allow-other-keys)
+                ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+                (let ((out (assoc-ref outputs "out"))
+                      (path (getenv "PERL5LIB")))
+                  (for-each
+                    (lambda (file)
+                      (wrap-program (string-append out "/bin/" file)
+                                    `("PERL5LIB" ":" prefix (,path))))
+                    '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls")))
+                #t))))))
+    (inputs
+     `(("gzip" ,gzip)
+       ,@(package-inputs edirect)))
+    (native-inputs
+     `(
+       ;("go" ,go)
+       ("xtract.Linux"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
+                               "versions/" (package-version edirect) "/xtract.Linux"))
+           (file-name (string-append "xtract.Linux-" (package-version edirect)))
+           (sha256
+            (base32
+             "0fx6arpn38spnwszmvkkpa3498qrrlglg2l9jw91icgqbyjjq9wq"))))
+       ("rchive.Linux"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
+                               "versions/" (package-version edirect) "/rchive.Linux"))
+           (file-name (string-append "rchive.Linux-" (package-version edirect)))
+           (sha256
+            (base32
+             "134y0zprplqlplc6qmcjb97411bxkwghmq3z0qjgh0dgdbzjq1w3"))))))
+    (native-search-paths
+     ;; Ideally this should be set for LWP somewhere.
+     (list (search-path-specification
+            (variable "PERL_LWP_SSL_CA_FILE")
+            (file-type 'regular)
+            (separator #f)
+            (files '("/etc/ssl/certs/ca-certificates.crt")))))
+    ;; Due to the precompiled binaries we download:
+    (supported-systems '("x86_64-linux"))))
+
+;; TODO: Unbundle zlib, bamtools, tclap
+(define-public sniffles
+  (package
+   (name "sniffles")
+   (version "1.0.11")
+   (source (origin
+     (method git-fetch)
+     (uri (git-reference
+            (url "https://github.com/fritzsedlazeck/Sniffles.git")
+            (commit version)))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32 "0rkwqn1ycckfzrg2wdid4cqahq8q2jmmgi7vvl8qxgpsihqfbq0j"))))
+   (build-system cmake-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (replace 'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((out (assoc-ref outputs "out")))
+              (install-file (string-append "../source/bin/sniffles-core-"
+                                           ,version "/sniffles")
+                            (string-append out "/bin")))
+            #t))
+        (replace 'check
+          (lambda _
+            (with-directory-excursion "../source/test_set"
+              (for-each make-file-writable (find-files "."))
+              (invoke (string-append "../bin/sniffles-core-" ,version "/sniffles")
+                      "-m" "reads_region.bam" "-v" "test.vcf")))))))
+   (native-inputs
+    `(("zlib" ,zlib)))
+   (home-page "https://github.com/fritzsedlazeck/Sniffles")
+   (synopsis "Structural variation caller using third generation sequencing")
+   (description
+    "Sniffles is a structural variation caller using third generation sequencing
+(PacBio or Oxford Nanopore).  It detects all types of SVs (10bp+) using evidence
+from split-read alignments, high-mismatch regions, and coverage analysis.")
+   (license license:expat)))
+
+;; TODO: Unbundle Complete-Striped-Smith-Waterman-Library
+(define-public ngmlr
+  (package
+   (name "ngmlr")
+   (version "0.2.7")
+   (source (origin
+     (method git-fetch)
+     (uri (git-reference
+            (url "https://github.com/philres/ngmlr.git")
+            (commit (string-append "v" version))))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32 "0lmsy8w0kxbyfnrln7lxgmnx3d82sv2b20n2yw5742rvfhq1v31n"))))
+   (build-system cmake-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-after 'patch-source-shebangs 'patch-more-tools
+          (lambda* (#:key inputs #:allow-other-keys)
+            (let ((bed (assoc-ref inputs "bedtools"))
+                  (sam (assoc-ref inputs "samtools")))
+              (substitute* (find-files "test" "\\.sh$")
+                (("bedtools") (string-append bed "/bin/bedtools"))
+                (("samtools") (string-append sam "/bin/samtools")))
+              #t)))
+        (replace 'check
+          (lambda _
+            (with-directory-excursion "../source"
+              (invoke "sh" "test/test_travis.sh")))))))
+   (native-inputs
+    `(("bedtools" ,bedtools)
+      ("samtools" ,samtools)))
+   (inputs
+    `(("zlib" ,zlib)))
+   (home-page "https://github.com/philres/ngmlr")
+   (synopsis "Long-read mapper designed to align PacBio or Oxford Nanopore")
+   (description
+    "NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore
+(standard and ultra-long) to a reference genome with a focus on reads that span
+structural variations.")
+   (license license:expat)))
+
+(define-public svim
+  (package
+   (name "svim")
+   (version "1.2.0")
+   (source (origin
+     (method git-fetch)
+     (uri (git-reference
+            (url "https://github.com/eldariont/svim.git")
+            (commit (string-append "v" version))))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32 "08j02in9jbq41b67dna1apnc3y30i37v44d1khml1xlx0iga720s"))))
+   (build-system python-build-system)
+   (arguments
+    '(#:phases
+      (modify-phases %standard-phases
+        (replace 'check
+          (lambda _
+            (invoke "python3" "-m" "unittest" "discover" "-s" "src/"))))))
+   (propagated-inputs
+    `(("python-matplotlib" ,python-matplotlib)
+      ("python-numpy" ,python-numpy)
+      ("python-pysam" ,python-pysam)
+      ("python-scipy" ,python-scipy)
+      ("minimap2" ,minimap2)
+      ("ngmlr" ,ngmlr)
+      ("samtools" ,samtools)))
+   (home-page "https://github.com/eldariont/svim")
+   (synopsis "Structural Variant Identification Method using Long Reads")
+   (description
+    "SVIM (pronounced SWIM) is a structural variant caller for long reads.  It
+is able to detect, classify and genotype five different classes of structural
+variants.  Unlike existing methods, SVIM integrates information from across the
+genome to precisely distinguish similar events, such as tandem and interspersed
+duplications and novel element insertions.")
+   (license license:gpl3)))