Merge remote-tracking branch 'origin/master' into staging

1 files changed, 303 insertions, 111 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4145d9e1f2..6f9580e9c3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1646,7 +1646,8 @@ gapped, local, and paired-end alignment modes.")
        (modify-phases %standard-phases
          (delete 'configure))))
     (inputs
-     `(("tbb" ,tbb)
+     `(("python-wrapper" ,python-wrapper)
+       ("tbb" ,tbb)
        ("zlib" ,zlib)))
     (supported-systems '("x86_64-linux"))
     (home-page "http://bowtie-bio.sourceforge.net/index.shtml")
@@ -1683,6 +1684,17 @@ genome (2.9 GB for paired-end).")
      '(#:parallel-build? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
+         (add-after 'set-paths 'hide-default-gcc
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gcc (assoc-ref inputs "gcc")))
+               ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent
+               ;; conflicts with the GCC 5 input.
+               (setenv "CPLUS_INCLUDE_PATH"
+                       (string-join
+                        (delete (string-append gcc "/include/c++")
+                                (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+                        ":"))
+               #t)))
          (add-after 'unpack 'use-system-samtools
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "src/Makefile.in"
@@ -1705,7 +1717,7 @@ genome (2.9 GB for paired-end).")
                (("#include <sam.h>") "#include <samtools/sam.h>"))
              #t)))))
     (native-inputs
-     `(("gcc" ,gcc-5))) ;; doesn't build with later versions
+     `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions
     (inputs
      `(("boost" ,boost)
        ("bowtie" ,bowtie)
@@ -2149,7 +2161,7 @@ databases.")
 (define-public clipper
   (package
     (name "clipper")
-    (version "1.2.1")
+    (version "2.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2158,40 +2170,34 @@ databases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; remove unnecessary setup dependency
-                  (substitute* "setup.py"
-                    (("setup_requires = .*") ""))
-                  #t))))
+                "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2 ; only Python 2 is supported
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
-         ;; This is fixed in upstream commit
-         ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.
-         (add-after 'unpack 'fix-typo
-           (lambda _
-             (substitute* "clipper/src/readsToWiggle.pyx"
-               (("^sc.*") ""))
-             #t)))))
+         (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))))))
     (inputs
-     `(("htseq" ,python2-htseq)
-       ("python-pybedtools" ,python2-pybedtools)
-       ("python-cython" ,python2-cython)
-       ("python-scikit-learn" ,python2-scikit-learn)
-       ("python-matplotlib" ,python2-matplotlib)
-       ("python-pandas" ,python2-pandas)
-       ("python-pysam" ,python2-pysam)
-       ("python-numpy" ,python2-numpy)
-       ("python-scipy" ,python2-scipy)))
+     `(("htseq" ,htseq)
+       ("python-pybedtools" ,python-pybedtools)
+       ("python-cython" ,python-cython)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pandas" ,python-pandas)
+       ("python-pysam" ,python-pysam)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
     (native-inputs
-     `(("python-mock" ,python2-mock)   ; for tests
-       ("python-nose" ,python2-nose)   ; for tests
-       ("python-pytz" ,python2-pytz))) ; for tests
+     `(("python-setuptools-git" ,python-setuptools-git)
+       ("python-mock" ,python-mock)   ; for tests
+       ("python-nose" ,python-nose)   ; for tests
+       ("python-pytz" ,python-pytz))) ; for tests
     (home-page "https://github.com/YeoLab/clipper")
     (synopsis "CLIP peak enrichment recognition")
     (description
@@ -2614,7 +2620,7 @@ with Python.")
 (define-public delly
   (package
     (name "delly")
-    (version "0.7.9")
+    (version "0.8.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2622,7 +2628,7 @@ with Python.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+               (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2646,9 +2652,9 @@ with Python.")
                #t))))))
     (inputs
      `(("boost" ,boost)
+       ("bzip2" ,bzip2)
        ("htslib" ,htslib)
-       ("zlib" ,zlib)
-       ("bzip2" ,bzip2)))
+       ("zlib" ,zlib)))
     (home-page "https://github.com/dellytools/delly")
     (synopsis "Integrated structural variant prediction method")
     (description "Delly is an integrated structural variant prediction method
@@ -3612,7 +3618,7 @@ particular, reads spanning multiple exons.")
     (native-inputs
      `(("unzip" ,unzip)                 ; needed for archive from ftp
        ("perl" ,perl)
-       ("pandoc" ,ghc-pandoc)))         ; for documentation
+       ("pandoc" ,pandoc)))             ; for documentation
     (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml")
     (synopsis "Graph-based alignment of genomic sequencing reads")
     (description "HISAT2 is a fast and sensitive alignment program for mapping
@@ -7505,13 +7511,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.56.1")
+    (version "1.56.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0zcx8gha3x3jc0ra6ii6wwq2vfsmffrrnilknbq8h5xjrl55m6ci"))))
+                "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7894,13 +7900,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.50.1")
+    (version "1.50.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "00pd8lsdppxlmx0l65phw0jhsm0qkwjc4wsdxpvgc31iiz9yslbj"))))
+                "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -8059,13 +8065,13 @@ tab-delimited (tabix) files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.14.0")
+    (version "0.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "1lz7a0rrlfv3w44n073mk8pw39z7lfs0njdxp5vpp0rdsmvdf1qk"))))
+                "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -8699,7 +8705,7 @@ paired-end data.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-s4vectors" ,r-s4vectors)
-       ("pandoc" ,ghc-pandoc)))
+       ("pandoc" ,pandoc)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (synopsis "RNA-centric annotation system")
@@ -9831,13 +9837,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.5")
+    (version "3.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
+                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9854,11 +9860,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
        ("r-irlba" ,r-irlba)
+       ("r-jsonlite" ,r-jsonlite)
        ("r-kernsmooth" ,r-kernsmooth)
        ("r-leiden" ,r-leiden)
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
+       ("r-miniui" ,r-miniui)
        ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
@@ -9876,7 +9884,9 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-rtsne" ,r-rtsne)
        ("r-scales" ,r-scales)
        ("r-sctransform" ,r-sctransform)
-       ("r-tsne" ,r-tsne)
+       ("r-shiny" ,r-shiny)
+       ("r-spatstat" ,r-spatstat)
+       ("r-tibble" ,r-tibble)
        ("r-uwot" ,r-uwot)))
     (home-page "http://www.satijalab.org/seurat")
     (synopsis "Seurat is an R toolkit for single cell genomics")
@@ -10018,14 +10028,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "2.20.0")
+    (version "2.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz"))))
+         "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10115,17 +10125,18 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.37.0")
+    (version "2.38.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr"))))
+         "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-go-db" ,r-go-db)
        ("r-graph" ,r-graph)
        ("r-keggrest" ,r-keggrest)))
     (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
@@ -10178,14 +10189,14 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.4.2")
+    (version "2.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l"))))
+         "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
@@ -11862,6 +11873,9 @@ straight away.  Its main features are:
               (snippet
                '(begin
                   (for-each delete-file (find-files "." "\\.exe$"))
+                  ;; Some files in the original tarball have restrictive
+                  ;; permissions, which makes repackaging fail
+                  (for-each (lambda (file) (chmod file #o644)) (find-files "."))
                   #t))))
     (build-system gnu-build-system)
     (arguments
@@ -12941,8 +12955,8 @@ once.  This package provides tools to perform Drop-seq analyses.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-rjson" ,r-rjson)
        ("salmon" ,salmon)
-       ("ghc-pandoc" ,ghc-pandoc)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
@@ -12958,7 +12972,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.42")
+    (version "0.0.43")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -12966,7 +12980,7 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0xbvgqpk32a8iczhvac56cacr46rdkqb0allhhpvmj940idf72bi"))))
+                "0426i31b7mqqkbss5dgrvf5prkj4z1qrd7yrpd27vybs01xhdlks"))))
     (build-system gnu-build-system)
     ;; parts of the tests rely on access to the network
     (arguments '(#:tests? #f))
@@ -13003,8 +13017,8 @@ expression report comparing samples in an easily configurable manner.")
        ("macs" ,macs)
        ("multiqc" ,multiqc)
        ("perl" ,perl)
-       ("ghc-pandoc" ,ghc-pandoc)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)
        ("fastqc" ,fastqc)
        ("bowtie" ,bowtie)
        ("idr" ,idr)
@@ -13028,7 +13042,7 @@ in an easily configurable manner.")
 (define-public pigx-bsseq
   (package
     (name "pigx-bsseq")
-    (version "0.0.10")
+    (version "0.1.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@@ -13036,10 +13050,13 @@ in an easily configurable manner.")
                                   "/pigx_bsseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy"))))
+                "0mpzlay2d5cjpmrcp7knff6rg1c2mqszd638n7lw0mc0cycbp9f8"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(;; TODO: tests currently require 12+GB of RAM.  See
+       ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
+       #:tests? #f
+       #:phases
        (modify-phases %standard-phases
          (add-before 'check 'set-timezone
            ;; The readr package is picky about timezones.
@@ -13059,22 +13076,27 @@ in an easily configurable manner.")
        ("r-annotationhub" ,r-annotationhub)
        ("r-dt" ,r-dt)
        ("r-genomation" ,r-genomation)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-methylkit" ,r-methylkit)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-bookdown" ,r-bookdown)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggbio" ,r-ggbio)
-       ("ghc-pandoc" ,ghc-pandoc)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("snakemake" ,snakemake)
        ("bismark" ,bismark)
-       ("fastqc" ,fastqc)
        ("bowtie" ,bowtie)
+       ("bwa-meth" ,bwa-meth)
+       ("fastqc" ,fastqc)
+       ("methyldackel" ,methyldackel)
+       ("multiqc" ,multiqc)
        ("trim-galore" ,trim-galore)
        ("cutadapt" ,cutadapt)
+       ("samblaster" ,samblaster)
        ("samtools" ,samtools)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
@@ -13110,8 +13132,8 @@ methylation and segmentation.")
        ("python-magic" ,python-magic)
        ("python-numpy" ,python-numpy)
        ("python-loompy" ,python-loompy)
-       ("ghc-pandoc" ,ghc-pandoc)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)
        ("samtools" ,samtools)
        ("snakemake" ,snakemake)
        ("star" ,star)
@@ -15378,12 +15400,34 @@ mutations from scRNA-Seq data.")
                       (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
                       (string-append "INCLUDES= -I" htslib-ref "/include/htslib")
                       "HTS_HEADERS="    ; No need to check for headers here.
-                      (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+                      (string-append "LIBPATH=-L. -L" htslib-ref "/include"))
+              (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
+              (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
-            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-              (install-file "tabix++" bin))
-            #t)))))
+            (let* ((out (assoc-ref outputs "out"))
+                   (lib (string-append out "/lib"))
+                   (bin (string-append out "/bin")))
+              (install-file "tabix++" bin)
+              (install-file "libtabixpp.so" lib)
+              (install-file "libtabixpp.a" lib)
+              (install-file "tabix.hpp" (string-append out "/include"))
+              (mkdir-p (string-append lib "/pkgconfig"))
+              (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
+                (lambda _
+                  (format #t "prefix=~a~@
+                          exec_prefix=${prefix}~@
+                          libdir=${exec_prefix}/lib~@
+                          includedir=${prefix}/include~@
+                          ~@
+                          ~@
+                          Name: libtabixpp~@
+                          Version: ~a~@
+                          Description: C++ wrapper around tabix project~@
+                          Libs: -L${libdir} -ltabixpp~@
+                          Cflags: -I${includedir}~%"
+                          out ,version)))
+              #t))))))
    (home-page "https://github.com/ekg/tabixpp")
    (synopsis "C++ wrapper around tabix project")
    (description "This is a C++ wrapper around the Tabix project which abstracts
@@ -15410,13 +15454,45 @@ some of the details of opening and jumping in tabix-indexed files.")
          #:phases
          (modify-phases %standard-phases
            (delete 'configure) ; There is no configure phase.
+           (add-after 'unpack 'patch-source
+             (lambda _
+               (substitute* "Makefile"
+                 (("-c ") "-c -fPIC "))
+               #t))
+           (add-after 'build 'build-dynamic
+             (lambda _
+               (invoke "g++"
+                       "-shared" "-o" "libsmithwaterman.so"
+                       "smithwaterman.o" "SmithWatermanGotoh.o"
+                       "disorder.o" "BandedSmithWaterman.o"
+                       "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin"))
                       (lib (string-append out "/lib")))
                  (install-file "smithwaterman" bin)
-                 (install-file "libsw.a" lib))
+                 (for-each
+                   (lambda (file)
+                     (install-file file (string-append out "/include/smithwaterman")))
+                   (find-files "." "\\.h$"))
+                 (install-file "libsmithwaterman.so" lib)
+                 (install-file "libsw.a" lib)
+                 (mkdir-p (string-append lib "/pkgconfig"))
+                 (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
+                   (lambda _
+                     (format #t "prefix=~a~@
+                             exec_prefix=${prefix}~@
+                             libdir=${exec_prefix}/lib~@
+                             includedir=${prefix}/include/smithwaterman~@
+                             ~@
+                             ~@
+                             Name: smithwaterman~@
+                             Version: ~a~@
+                             Description: smith-waterman-gotoh alignment algorithm~@
+                             Libs: -L${libdir} -lsmithwaterman~@
+                             Cflags: -I${includedir}~%"
+                             out ,version))))
                #t)))))
       (home-page "https://github.com/ekg/smithwaterman")
       (synopsis "Implementation of the Smith-Waterman algorithm")
@@ -15506,10 +15582,43 @@ neural networks.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
+           (add-after 'unpack 'patch-source
+             (lambda _
+               (substitute* "Makefile"
+                 (("-c ") "-c -fPIC "))
+               #t))
+         (add-after 'build 'build-dynamic
+           (lambda _
+             (invoke "g++"
+                     "-shared" "-o" "libfastahack.so"
+                     "Fasta.o" "FastaHack.o" "split.o" "disorder.o")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-               (install-file "fastahack" bin))
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib"))
+                    (bin (string-append out "/bin")))
+               (mkdir-p (string-append out "/include/fastahack"))
+               (for-each
+                 (lambda (file)
+                   (install-file file (string-append out "/include/fastahack")))
+                 (find-files "." "\\.h$"))
+               (install-file "fastahack" bin)
+               (install-file "libfastahack.so" lib)
+               (mkdir-p (string-append lib "/pkgconfig"))
+               (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc")
+                 (lambda _
+                   (format #t "prefix=~a~@
+                           exec_prefix=${prefix}~@
+                           libdir=${exec_prefix}/lib~@
+                           includedir=${prefix}/include/fastahack~@
+                           ~@
+                           ~@
+                           Name: fastahack~@
+                           Version: ~a~@
+                           Description: Indexing and sequence extraction from FASTA files~@
+                           Libs: -L${libdir} -lfastahack~@
+                           Cflags: -I${includedir}~%"
+                           out ,version))))
              #t)))))
     (home-page "https://github.com/ekg/fastahack")
     (synopsis "Indexing and sequence extraction from FASTA files")
@@ -15532,9 +15641,16 @@ library automatically handles index file generation and use.")
                            "/vcflib-" version "-src.tar.gz"))
        (sha256
         (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+       (patches (search-patches "vcflib-use-shared-libraries.patch"))
        (modules '((guix build utils)))
        (snippet
         `(begin
+           (substitute* (find-files "." "\\.(h|c)(pp)?$")
+             (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
+             (("\"convert.h\"") "<smithwaterman/convert.h>")
+             (("\"disorder.h\"") "<smithwaterman/disorder.h>")
+             (("\"tabix.hpp\"") "<tabix.hpp>")
+             (("\"Fasta.h\"") "<fastahack/Fasta.h>"))
            (for-each delete-file-recursively
                      '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
                        "libVCFH" "multichoose" "smithwaterman" "tabixpp"))
@@ -15542,34 +15658,34 @@ library automatically handles index file generation and use.")
     (build-system gnu-build-system)
     (inputs
      `(("htslib" ,htslib)
+       ("fastahack" ,fastahack)
        ("perl" ,perl)
        ("python" ,python)
+       ("smithwaterman" ,smithwaterman)
+       ("tabixpp" ,tabixpp)
+       ("xz" ,xz)
        ("zlib" ,zlib)))
     (native-inputs
-     `(;; Submodules.
+     `(("pkg-config" ,pkg-config)
+       ;; Submodules.
        ;; This package builds against the .o files so we need to extract the source.
-       ("fastahack-src" ,(package-source fastahack))
        ("filevercmp-src" ,(package-source filevercmp))
-       ("fsom-src" ,(package-source fsom))
        ("intervaltree-src" ,(package-source intervaltree))
-       ("multichoose-src" ,(package-source multichoose))
-       ("smithwaterman-src" ,(package-source smithwaterman))
-       ("tabixpp-src" ,(package-source tabixpp))))
+       ("multichoose-src" ,(package-source multichoose))))
     (arguments
      `(#:tests? #f ; no tests
-       #:make-flags (list (string-append "HTS_LIB="
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/lib/libhts.a")
-                          (string-append "HTS_INCLUDES= -I"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib")
-                          (string-append "HTS_LDFLAGS= -L"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib" " -lhts"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'set-flags
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("LDFLAGS =")
+                (string-append "LDFLAGS = -Wl,-rpath="
+                               (assoc-ref outputs "out") "/lib ")))
+             (substitute* "filevercmp/Makefile"
+               (("-c") "-c -fPIC"))
+             #t))
          (delete 'configure)
-         (delete 'check)
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((unpack (lambda (source target)
@@ -15581,34 +15697,39 @@ library automatically handles index file generation and use.")
                                            (assoc-ref inputs source)
                                            "--strip-components=1"))))))
                (and
-                (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")))))
-         (replace 'build
-           (lambda* (#:key inputs make-flags #:allow-other-keys)
-             (let ((htslib (assoc-ref inputs "htslib")))
-               (with-directory-excursion "tabixpp"
-                 (substitute* "Makefile"
-                   (("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
-                   (("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
-                   (("htslib/htslib") (string-append htslib "/include/htslib")))
-                 (invoke "make"
-                         (string-append "HTS_LIB=" htslib "/lib/libhts.a")))
-               (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
+                (unpack "multichoose-src" "multichoose")))))
          (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")))
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (lib (string-append 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))
+               (install-file "libvcflib.so" lib)
+               (install-file "libvcflib.a" lib)
+               (for-each
+                 (lambda (file)
+                   (install-file file (string-append out "/include")))
+                 (find-files "include" "\\.h(pp)?$"))
+               (mkdir-p (string-append lib "/pkgconfig"))
+               (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc")
+                 (lambda _
+                   (format #t "prefix=~a~@
+                           exec_prefix=${prefix}~@
+                           libdir=${exec_prefix}/lib~@
+                           includedir=${prefix}/include~@
+                           ~@
+                           ~@
+                           Name: libvcflib~@
+                           Version: ~a~@
+                           Requires: smithwaterman, fastahack~@
+                           Description: C++ library for parsing and manipulating VCF files~@
+                           Libs: -L${libdir} -lvcflib~@
+                           Cflags: -I${includedir}~%"
+                           out ,version))))
              #t)))))
     (home-page "https://github.com/vcflib/vcflib/")
     (synopsis "Library for parsing and manipulating VCF files")
@@ -15862,6 +15983,77 @@ containing the reference genome as well.")
     ;; See https://github.com/dpryan79/MethylDackel/issues/85
     (license license:expat)))
 
+;; This package bundles PCRE 8.02 and cannot be built with the current
+;; version.
+(define-public phast
+  (package
+    (name "phast")
+    (version "1.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/CshlSiepelLab/phast")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list "CC=gcc"
+             (string-append "DESTDIR=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Fix syntax
+             (substitute* "test/Makefile"
+               (("        ") "	"))
+             (substitute* "Makefile"
+               (("CLAPACKPATH=/usr/lib")
+                (string-append "CLAPACKPATH="
+                               (assoc-ref inputs "clapack") "/lib")))
+             ;; Renaming the libraries is not necessary with our version of
+             ;; CLAPACK.
+             (substitute* "src/lib/Makefile"
+               (("ifdef CLAPACKPATH") "ifdef UNNECESSARY"))
+             (substitute* "src/make-include.mk"
+               (("-lblaswr") "-lblas")
+               (("-ltmg") "-ltmglib")
+               (("liblapack.a") "liblapack.so")
+               (("libblas.a") "libblas.so")
+               (("libf2c.a") "libf2c.so"))
+             (substitute* "src/Makefile"
+               (("/opt") "/share")
+               (("/usr/") "/"))
+             #t))
+         (replace 'check
+           (lambda _
+             (setenv "PATH"
+                     (string-append (getcwd) "/bin:" (getenv "PATH")))
+             ;; Disable broken test
+             (substitute* "test/Makefile"
+               ((".*if.*hmrc_summary" m) (string-append "#" m)))
+             ;; Only run the msa_view tests because the others fail for
+             ;; unknown reasons.
+             (invoke "make" "-C" "test" "msa_view"))))))
+    (inputs
+     `(("clapack" ,clapack)))
+    (native-inputs
+     `(("perl" ,perl)))
+    (home-page "http://compgen.cshl.edu/phast/")
+    (synopsis "Phylogenetic analysis with space/time models")
+    (description
+     "Phylogenetic Analysis with Space/Time models (PHAST) is a collection of
+command-line programs and supporting libraries for comparative and
+evolutionary genomics.  Best known as the search engine behind the
+Conservation tracks in the University of California, Santa Cruz (UCSC) Genome
+Browser, PHAST also includes several tools for phylogenetic modeling,
+functional element identification, as well as utilities for manipulating
+alignments, trees and genomic annotations.")
+    (license license:bsd-3)))
+
 (define-public python-gffutils
   ;; The latest release is older more than a year than the latest commit
   (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1")