Merge branch 'master' into core-updates

1 files changed, 433 insertions, 22 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b1cf294177..898b8d200e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4195,8 +4196,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
        (modify-phases %standard-phases
          (add-after 'unpack 'set-cc
            (lambda _ (setenv "CC" "gcc") #t))
-         ;; FIXME: This fails with "permission denied".
-         (delete 'reset-gzip-timestamps))))
+
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure .gz files are writable so that the
+             ;; 'reset-gzip-timestamps' phase can do its work.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
     (native-inputs
      `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)
@@ -7439,13 +7447,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.26.5")
+    (version "3.26.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+                "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7506,13 +7514,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.40.2")
+    (version "3.40.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+                "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7639,13 +7647,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.40.1")
+    (version "2.40.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+                "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7672,13 +7680,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.18.0")
+    (version "1.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
+                "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7800,13 +7808,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+                "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7864,13 +7872,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.44.0")
+    (version "1.44.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+                "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7911,13 +7919,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.36.3")
+    (version "1.36.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+                "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8335,13 +8343,13 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+                "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9399,14 +9407,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+         "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10406,14 +10414,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.12.1")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp"))))
+         "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -14804,3 +14812,406 @@ trees by inserting random mutations.  The tbsp package implements an
 alternative method to detect significant, cell type specific sequence
 mutations from scRNA-Seq data.")
       (license license:expat))))
+
+(define-public tabixpp
+  (package
+   (name "tabixpp")
+   (version "1.0.0")
+   (source (origin
+     (method git-fetch)
+     (uri (git-reference
+           (url "https://github.com/ekg/tabixpp")
+           (commit (string-append "v" version))))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
+   (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")))
+              (invoke "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))
+            #t)))))
+   (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)))
+
+(define tabixpp-freebayes
+  ;; 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.
+  (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+    (package
+      (inherit tabixpp)
+      (name "tabixpp-freebayes")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/tabixpp/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
+
+(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 git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/smithwaterman/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+      (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))
+               #t)))))
+      (home-page "https://github.com/ekg/smithwaterman")
+      (synopsis "Implementation of the Smith-Waterman algorithm")
+      (description "Implementation of the Smith-Waterman algorithm.")
+      ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
+      (license (list license:gpl2 license:expat)))))
+
+(define-public multichoose
+  (package
+    (name "multichoose")
+    (version "1.0.3")
+    (source (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/ekg/multichoose/")
+            (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; Tests require node.
+       #: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))
+             #t)))))
+    (home-page "https://github.com/ekg/multichoose")
+    (synopsis "Efficient loopless multiset combination generation algorithm")
+    (description "This 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 (git-version "0.0.0" "1" commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/fsom/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
+      (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))
+               #t)))))
+      (home-page "https://github.com/ekg/fsom")
+      (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
+      (description "A tiny C library for managing SOM (Self-Organizing Maps)
+neural networks.")
+      (license license:gpl3))))
+
+(define-public fastahack
+  (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
+    (package
+      (name "fastahack")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/fastahack/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
+         #: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))
+               #t)))))
+      (home-page "https://github.com/ekg/fastahack")
+      (synopsis "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 library
+provides a FASTA reader and indexer that can be embedded into applications
+which would benefit from directly reading subsequences from FASTA files.  The
+library automatically handles index file generation and use.")
+      (license (list license:expat license:gpl2)))))
+
+(define-public vcflib
+  (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
+        (revision "1"))
+    (package
+      (name "vcflib")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vcflib/vcflib/")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
+      (build-system gnu-build-system)
+      (inputs
+       `(("zlib" ,zlib)))
+      (native-inputs
+       `(("perl" ,perl)
+         ("python" ,python-2)
+         ;; Submodules.
+         ;; 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"))))))
+      (arguments
+       `(#:tests? #f ; no tests
+         #: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
+                                 (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 "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")))))
+           (replace 'build
+             (lambda* (#:key inputs make-flags #:allow-other-keys)
+               (with-directory-excursion "tabixpp"
+                 (invoke "make"))
+               (invoke "make" "CC=gcc"
+                       (string-append "CFLAGS=\"" "-Itabixpp " "\"")
+                       "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" ".*"))
+                 ;; The header files in src/ do not interface libvcflib,
+                 ;; therefore they are left out.
+                 (install-file "libvcflib.a" lib))
+               #t)))))
+      (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 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
+       `(("bamtools" ,bamtools)
+         ("htslib" ,htslib)
+         ("zlib" ,zlib)))
+      (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.
+         ("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
+       `(#:make-flags
+         (list "CC=gcc"
+               (string-append "BAMTOOLS_ROOT="
+                              (assoc-ref %build-inputs "bamtools")))
+         #:test-target "test"
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-after 'unpack 'fix-tests
+             (lambda _
+               (substitute* "test/t/01_call_variants.t"
+                 (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
+                  "grep -E '	(500|11000|1000)$'"))
+               #t))
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (if (file-is-directory? (assoc-ref inputs source))
+                                     (copy-recursively (assoc-ref inputs source) ".")
+                                     (invoke "tar" "xvf"
+                                             (assoc-ref inputs source)
+                                             "--strip-components=1"))))))
+                 (and
+                  (unpack "vcflib-src" "vcflib")
+                  (unpack "fastahack-src" "vcflib/fastahack")
+                  (unpack "filevercmp-src" "vcflib/filevercmp")
+                  (unpack "fsom-src" "vcflib/fsom")
+                  (unpack "intervaltree-src" "vcflib/intervaltree")
+                  (unpack "multichoose-src" "vcflib/multichoose")
+                  (unpack "smithwaterman-src" "vcflib/smithwaterman")
+                  (unpack "tabixpp-src" "vcflib/tabixpp")
+                  (unpack "test-simple-bash-src" "test/test-simple-bash")
+                  (unpack "bash-tap-src" "test/bash-tap")))))
+           (add-after 'unpack-submodule-sources 'fix-makefiles
+             (lambda _
+               ;; We don't have the .git folder to get the version tag from.
+               (substitute* "vcflib/Makefile"
+                 (("^GIT_VERSION.*")
+                  (string-append "GIT_VERSION = v" ,version)))
+               (substitute* "src/Makefile"
+                 (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
+                  "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+               #t))
+           (add-before 'build 'build-tabixpp-and-vcflib
+             (lambda* (#:key inputs make-flags #:allow-other-keys)
+               (with-directory-excursion "vcflib"
+                 (with-directory-excursion "tabixpp"
+                   (apply invoke "make"
+                          (string-append "HTS_LIB="
+                                         (assoc-ref inputs "htslib")
+                                         "/lib/libhts.a")
+                          make-flags))
+                 (apply invoke "make"
+                        (string-append "CFLAGS=-Itabixpp")
+                        "all"
+                        make-flags))))
+           (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))))