Merge branch 'master' into core-updates

1 files changed, 205 insertions, 113 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91bb94c549..1e04081ceb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -136,24 +136,23 @@
        (modify-phases %standard-phases
          (delete 'configure)
          (replace 'build
-                  (lambda _
-                    (zero? (system* "gcc"
-                                    "-O3"
-                                    "-ffast-math"
-                                    "-finline-functions"
-                                    "-o"
-                                    "aragorn"
-                                    (string-append "aragorn" ,version ".c")))))
+           (lambda _
+             (invoke "gcc"
+                     "-O3"
+                     "-ffast-math"
+                     "-finline-functions"
+                     "-o"
+                     "aragorn"
+                     (string-append "aragorn" ,version ".c"))
+             #t))
          (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let* ((out (assoc-ref outputs "out"))
-                           (bin (string-append out "/bin"))
-                           (man (string-append out "/share/man/man1")))
-                      (mkdir-p bin)
-                      (install-file "aragorn" bin)
-                      (mkdir-p man)
-                      (install-file "aragorn.1" man))
-                    #t)))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1")))
+               (install-file "aragorn" bin)
+               (install-file "aragorn.1" man))
+             #t)))))
     (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
     (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
     (description
@@ -168,15 +167,16 @@ structure of the predicted RNA.")
     (name "bamm")
     (version "1.7.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
               ;; BamM is not available on pypi.
-              (uri (string-append
-                    "https://github.com/Ecogenomics/BamM/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (git-reference
+                    (url "https://github.com/Ecogenomics/BamM.git")
+                    (commit version)
+                    (recursive? #t)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
+                "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
               (modules '((guix build utils)))
               (snippet
                `(begin
@@ -198,11 +198,12 @@ structure of the predicted RNA.")
            (lambda _
              (with-directory-excursion "c"
                (let ((sh (which "sh")))
+                 (for-each make-file-writable (find-files "." ".*"))
                  ;; Use autogen so that 'configure' works.
                  (substitute* "autogen.sh" (("/bin/sh") sh))
                  (setenv "CONFIG_SHELL" sh)
-                 (substitute* "configure" (("/bin/sh") sh))
-                 (zero? (system* "./autogen.sh"))))))
+                 (invoke "./autogen.sh")))
+             #t))
          (delete 'build)
          ;; Run tests after installation so compilation only happens once.
          (delete 'check)
@@ -230,7 +231,8 @@ structure of the predicted RNA.")
              ;; There are 2 errors printed, but they are safe to ignore:
              ;; 1) [E::hts_open_format] fail to open file ...
              ;; 2) samtools view: failed to open ...
-             (zero? (system* "nosetests")))))))
+             (invoke "nosetests")
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -335,15 +337,16 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 (define-public bedops
   (package
     (name "bedops")
-    (version "2.4.33")
+    (version "2.4.35")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/bedops/bedops/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bedops/bedops.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
+                "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -365,9 +368,9 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 
              ;; Unpack the tarballs to benefit from shebang patching.
              (with-directory-excursion "third-party"
-               (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
-                    (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
-                    (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
+               (invoke "tar" "xvf" "jansson-2.6.tar.bz2")
+               (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
+               (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
              ;; Disable unpacking of tarballs in Makefile.
              (substitute* "system.mk/Makefile.linux"
                (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
@@ -453,6 +456,20 @@ BED, GFF/GTF, VCF.")
                          (find-files "bin" ".*")))
              #t)))))))
 
+;; Needed for pybedtools.
+(define-public bedtools-2.26
+  (package (inherit bedtools)
+    (name "bedtools")
+    (version "2.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
+                                  "download/v" version "/"
+                                  "bedtools-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5"))))))
+
 (define-public ribotaper
   (package
     (name "ribotaper")
@@ -582,29 +599,54 @@ input/output delimiter.  When the new functionality is not used, bioawk is
 intended to behave exactly the same as the original BWK awk.")
     (license license:x11)))
 
-(define-public python2-pybedtools
+(define-public python-pybedtools
   (package
-    (name "python2-pybedtools")
-    (version "0.6.9")
+    (name "python-pybedtools")
+    (version "0.7.10")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
-                    version ".tar.gz"))
+              (uri (pypi-uri "pybedtools" version))
               (sha256
                (base32
-                "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
+                "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; no Python 3 support
-    (inputs
-     `(("python-matplotlib" ,python2-matplotlib)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/daler/pybedtools/issues/261
+         (add-after 'unpack 'disable-broken-tests
+           (lambda _
+             ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a
+             ;; graphical environment.
+             (substitute* "pybedtools/test/test_scripts.py"
+               (("def test_venn_mpl")
+                "def _do_not_test_venn_mpl"))
+             ;; Requires internet access.
+             (substitute* "pybedtools/test/test_helpers.py"
+               (("def test_chromsizes")
+                "def _do_not_test_chromsizes"))
+             ;; FIXME: these two fail for no good reason.
+             (substitute* "pybedtools/test/test1.py"
+               (("def test_issue_157")
+                "def _do_not_test_issue_157")
+               (("def test_to_dataframe")
+                "def _do_not_test_to_dataframe"))
+             #t)))))
     (propagated-inputs
-     `(("bedtools" ,bedtools)
-       ("samtools" ,samtools)))
+     ;; Tests don't pass with Bedtools 2.27.1.
+     ;; See https://github.com/daler/pybedtools/issues/260
+     `(("bedtools" ,bedtools-2.26)
+       ("samtools" ,samtools)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pysam" ,python-pysam)
+       ("python-pyyaml" ,python-pyyaml)))
     (native-inputs
-     `(("python-cython" ,python2-cython)
-       ("python-pyyaml" ,python2-pyyaml)
-       ("python-nose" ,python2-nose)))
+     `(("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-cython" ,python-cython)
+       ("python-nose" ,python-nose)
+       ("kentutils" ,kentutils) ; for bedGraphToBigWig
+       ("python-six" ,python-six)))
     (home-page "https://pythonhosted.org/pybedtools/")
     (synopsis "Python wrapper for BEDtools programs")
     (description
@@ -614,6 +656,36 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public python2-pybedtools
+  (let ((pkg (package-with-python2 python-pybedtools)))
+    (package (inherit pkg)
+      (arguments
+       `(#:modules ((ice-9 ftw)
+                    (srfi srfi-1)
+                    (srfi srfi-26)
+                    (guix build utils)
+                    (guix build python-build-system))
+         ;; See https://github.com/daler/pybedtools/issues/192
+         ,@(substitute-keyword-arguments (package-arguments pkg)
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (replace 'check
+                   (lambda _
+                     (let ((cwd (getcwd)))
+                       (setenv "PYTHONPATH"
+                               (string-append cwd "/build/"
+                                              (find (cut string-prefix? "lib" <>)
+                                                    (scandir (string-append cwd "/build")))
+                                              ":" (getenv "PYTHONPATH"))))
+                     ;; The tests need to be run from elsewhere...
+                     (mkdir-p "/tmp/test")
+                     (copy-recursively "pybedtools/test" "/tmp/test")
+                     (with-directory-excursion "/tmp/test"
+                       (invoke "nosetests"
+                               ;; This test fails for unknown reasons
+                               "--exclude=.*test_getting_example_beds"))
+                     #t))))))))))
+
 (define-public python-biom-format
   (package
    (name "python-biom-format")
@@ -999,15 +1071,12 @@ package provides command line tools using the Bio++ library.")
        #:parallel-build? #f ; not supported
        #:phases
        (modify-phases %standard-phases
-         (add-before
-          'configure 'set-HOME
+         (add-before 'configure 'set-HOME
           ;; $HOME needs to be set at some point during the configure phase
           (lambda _ (setenv "HOME" "/tmp") #t))
-         (add-after
-          'unpack 'enter-dir
+         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "c++") #t))
-         (add-after
-          'enter-dir 'fix-build-system
+         (add-after 'enter-dir 'fix-build-system
           (lambda _
             (define (which* cmd)
               (cond ((string=? cmd "date")
@@ -1055,31 +1124,31 @@ package provides command line tools using the Bio++ library.")
               (("action=/bin/") "action=")
               (("export PATH") ":"))
             #t))
-         (replace
-          'configure
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            (let ((out     (assoc-ref outputs "out"))
-                  (lib     (string-append (assoc-ref outputs "lib") "/lib"))
-                  (include (string-append (assoc-ref outputs "include")
-                                          "/include/ncbi-tools++")))
-              ;; The 'configure' script doesn't recognize things like
-              ;; '--enable-fast-install'.
-              (zero? (system* "./configure.orig"
-                              (string-append "--with-build-root=" (getcwd) "/build")
-                              (string-append "--prefix=" out)
-                              (string-append "--libdir=" lib)
-                              (string-append "--includedir=" include)
-                              (string-append "--with-bz2="
-                                             (assoc-ref inputs "bzip2"))
-                              (string-append "--with-z="
-                                             (assoc-ref inputs "zlib"))
-                              (string-append "--with-pcre="
-                                             (assoc-ref inputs "pcre"))
-                              ;; Each library is built twice by default, once
-                              ;; with "-static" in its name, and again
-                              ;; without.
-                              "--without-static"
-                              "--with-dll"))))))))
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out     (assoc-ref outputs "out"))
+                   (lib     (string-append (assoc-ref outputs "lib") "/lib"))
+                   (include (string-append (assoc-ref outputs "include")
+                                           "/include/ncbi-tools++")))
+               ;; The 'configure' script doesn't recognize things like
+               ;; '--enable-fast-install'.
+               (invoke "./configure.orig"
+                       (string-append "--with-build-root=" (getcwd) "/build")
+                       (string-append "--prefix=" out)
+                       (string-append "--libdir=" lib)
+                       (string-append "--includedir=" include)
+                       (string-append "--with-bz2="
+                                      (assoc-ref inputs "bzip2"))
+                       (string-append "--with-z="
+                                      (assoc-ref inputs "zlib"))
+                       (string-append "--with-pcre="
+                                      (assoc-ref inputs "pcre"))
+                       ;; Each library is built twice by default, once
+                       ;; with "-static" in its name, and again
+                       ;; without.
+                       "--without-static"
+                       "--with-dll")
+               #t))))))
     (outputs '("out"       ;  21 MB
                "lib"       ; 226 MB
                "include")) ;  33 MB
@@ -1204,15 +1273,16 @@ errors at the end of reads.")
 (define-public bowtie
   (package
     (name "bowtie")
-    (version "2.3.2")
+    (version "2.3.4.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BenLangmead/bowtie2.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
+                "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1222,14 +1292,6 @@ errors at the end of reads.")
                     (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
                   #t))))
     (build-system gnu-build-system)
-    (inputs
-     `(("perl" ,perl)
-       ("perl-clone" ,perl-clone)
-       ("perl-test-deep" ,perl-test-deep)
-       ("perl-test-simple" ,perl-test-simple)
-       ("python" ,python-2)
-       ("tbb" ,tbb)
-       ("zlib" ,zlib)))
     (arguments
      '(#:make-flags
        (list "allall"
@@ -1239,11 +1301,21 @@ errors at the end of reads.")
        (modify-phases %standard-phases
          (delete 'configure)
          (replace 'check
-           (lambda* (#:key outputs #:allow-other-keys)
-             (zero? (system* "perl"
-                             "scripts/test/simple_tests.pl"
-                             "--bowtie2=./bowtie2"
-                             "--bowtie2-build=./bowtie2-build")))))))
+           (lambda _
+             (invoke "perl"
+                     "scripts/test/simple_tests.pl"
+                     "--bowtie2=./bowtie2"
+                     "--bowtie2-build=./bowtie2-build")
+             #t)))))
+    (inputs
+     `(("tbb" ,tbb)
+       ("zlib" ,zlib)
+       ("python" ,python-wrapper)))
+    (native-inputs
+     `(("perl" ,perl)
+       ("perl-clone" ,perl-clone)
+       ("perl-test-deep" ,perl-test-deep)
+       ("perl-test-simple" ,perl-test-simple)))
     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
     (synopsis "Fast and sensitive nucleotide sequence read aligner")
     (description
@@ -1638,29 +1710,35 @@ databases.")
 (define-public clipper
   (package
     (name "clipper")
-    (version "1.1")
+    (version "1.2.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/YeoLab/clipper/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/YeoLab/clipper.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
+                "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; remove unnecessary setup dependency
                   (substitute* "setup.py"
                     (("setup_requires = .*") ""))
-                  (for-each delete-file
-                            '("clipper/src/peaks.so"
-                              "clipper/src/readsToWiggle.so"))
-                  (delete-file-recursively "dist/")
                   #t))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; only Python 2 is supported
+    (arguments
+     `(#:python ,python-2 ; only Python 2 is supported
+       #: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)))))
     (inputs
      `(("htseq" ,python2-htseq)
        ("python-pybedtools" ,python2-pybedtools)
@@ -1985,7 +2063,21 @@ trees (phylogenies) and characters.")
     (license license:bsd-3)))
 
 (define-public python2-dendropy
-  (package-with-python2 python-dendropy))
+  (let ((base (package-with-python2 python-dendropy)))
+    (package
+      (inherit base)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'remove-failing-test
+             (lambda _
+               ;; This test fails when the full test suite is run, as documented
+               ;; at https://github.com/jeetsukumaran/DendroPy/issues/74
+               (substitute* "tests/test_dataio_nexml_reader_tree_list.py"
+                 (("test_collection_comments_and_annotations")
+                  "do_not_test_collection_comments_and_annotations"))
+               #t)))
+         ,@(package-arguments base))))))
 
 (define-public python-py2bit
   (package