Merge branch 'master' into core-updates

1 files changed, 160 insertions, 59 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e74abf005f..d48f484e03 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -288,34 +288,25 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.8")
+    (version "1.9")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://github.com/samtools/bcftools/releases/download/"
-                    version "/bcftools-" version ".tar.bz2"))
+              (uri (string-append "https://github.com/samtools/bcftools/"
+                                  "releases/download/"
+                                  version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
+                "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Delete bundled htslib.
-                          (delete-file-recursively "htslib-1.8")
+                          (delete-file-recursively "htslib-1.9")
                           #t))))
     (build-system gnu-build-system)
     (arguments
-     `(#:test-target "test"
-       #:configure-flags (list "--with-htslib=system")
-       #:make-flags
-       (list
-        "USE_GPL=1"
-        "LIBS=-lgsl -lgslcblas"
-        (string-append "prefix=" (assoc-ref %outputs "out"))
-        (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
-        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
-        (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
-        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
-        (string-append "PACKAGE_VERSION=" ,version))
+     `(#:configure-flags
+       (list "--enable-libgsl")
+       #:test-target "test"
        #:phases
        (modify-phases %standard-phases
          (add-before 'check 'patch-tests
@@ -1445,17 +1436,17 @@ multiple sequence alignments.")
 (define-public python-pysam
   (package
     (name "python-pysam")
-    (version "0.13.0")
+    (version "0.15.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
               ;; Test data is missing on PyPi.
-              (uri (string-append
-                    "https://github.com/pysam-developers/pysam/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (git-reference
+                    (url "https://github.com/pysam-developers/pysam.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
+                "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Drop bundled htslib. TODO: Also remove samtools
@@ -1482,6 +1473,11 @@ multiple sequence alignments.")
              #t))
          (replace 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; This file contains tests that require a connection to the
+             ;; internet.
+             (delete-file "tests/tabix_test.py")
+             ;; FIXME: This test fails
+             (delete-file "tests/AlignmentFile_test.py")
              ;; Add first subdirectory of "build" directory to PYTHONPATH.
              (setenv "PYTHONPATH"
                      (string-append
@@ -1492,28 +1488,26 @@ multiple sequence alignments.")
              ;; Step out of source dir so python does not import from CWD.
              (with-directory-excursion "tests"
                (setenv "HOME" "/tmp")
-               (and (zero? (system* "make" "-C" "pysam_data"))
-                    (zero? (system* "make" "-C" "cbcf_data"))
-                    ;; Running nosetests without explicitly asking for a
-                    ;; single process leads to a crash.  Running with multiple
-                    ;; processes fails because the tests are not designed to
-                    ;; run in parallel.
-
-                    ;; FIXME: tests keep timing out on some systems.
-                    ;; (zero? (system* "nosetests" "-v"
-                    ;;                 "--processes" "1"))
-                    )))))))
-    (propagated-inputs
-     `(("htslib"            ,htslib))) ; Included from installed header files.
+               (invoke "make" "-C" "pysam_data")
+               (invoke "make" "-C" "cbcf_data")
+               ;; Running nosetests without explicitly asking for a single
+               ;; process leads to a crash.  Running with multiple processes
+               ;; fails because the tests are not designed to run in parallel.
+
+               ;; FIXME: tests keep timing out on some systems.
+               (invoke "nosetests" "-v" "--processes" "1")))))))
+    (propagated-inputs
+     `(("htslib" ,htslib))) ; Included from installed header files.
     (inputs
-     `(("ncurses"           ,ncurses)
-       ("zlib"              ,zlib)))
+     `(("ncurses" ,ncurses)
+       ("curl" ,curl)
+       ("zlib" ,zlib)))
     (native-inputs
-     `(("python-cython"     ,python-cython)
+     `(("python-cython" ,python-cython)
        ;; Dependencies below are are for tests only.
-       ("samtools"          ,samtools)
-       ("bcftools"          ,bcftools)
-       ("python-nose"       ,python-nose)))
+       ("samtools" ,samtools)
+       ("bcftools" ,bcftools)
+       ("python-nose" ,python-nose)))
     (home-page "https://github.com/pysam-developers/pysam")
     (synopsis "Python bindings to the SAMtools C API")
     (description
@@ -2012,18 +2006,25 @@ with Python.")
 (define-public deeptools
   (package
     (name "deeptools")
-    (version "2.5.1")
+    (version "3.1.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/deeptools/deepTools/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/deeptools/deepTools.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
+                "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This phase fails, but it's not needed.
+         (delete 'reset-gzip-timestamps))))
     (inputs
-     `(("python-scipy" ,python-scipy)
+     `(("python-plotly" ,python-plotly)
+       ("python-scipy" ,python-scipy)
        ("python-numpy" ,python-numpy)
        ("python-numpydoc" ,python-numpydoc)
        ("python-matplotlib" ,python-matplotlib)
@@ -3512,7 +3513,7 @@ performance.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.8")
+    (version "1.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3520,7 +3521,7 @@ performance.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
+                "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
     (build-system gnu-build-system)
     (inputs
      `(("openssl" ,openssl)
@@ -4997,7 +4998,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
@@ -5006,15 +5007,19 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
+         "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   ;; Delete bundled htslib.
+                   (delete-file-recursively "htslib-1.9")
+                   #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
                   (ice-9 regex)
                   (guix build gnu-build-system)
                   (guix build utils))
-       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
-       #:configure-flags (list "--with-ncurses" "--with-htslib=system")
+       #:configure-flags (list "--with-ncurses")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-tests
@@ -5068,9 +5073,9 @@ viewer.")
         (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
     (arguments
      `(#:tests? #f ;no "check" target
+       #:make-flags
+       (list "LIBCURSES=-lncurses")
        ,@(substitute-keyword-arguments (package-arguments samtools)
-           ((#:make-flags flags)
-            `(cons "LIBCURSES=-lncurses" ,flags))
            ((#:phases phases)
             `(modify-phases ,phases
                (replace 'install
@@ -13869,3 +13874,99 @@ single-cell transcriptomic map of the human and mouse pancreas reveals inter-
 and intra-cell population structure.\" Baron et al. Cell Systems (2016)
 @url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
       (license license:gpl2+))))
+
+(define-public porechop
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Porechop#installation
+  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
+        (revision "1"))
+    (package
+      (name "porechop")
+      (version (git-version "0.2.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Porechop.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
+      (build-system python-build-system)
+      (home-page "https://github.com/rrwick/porechop")
+      (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
+      (description
+       "The porechop package is a tool for finding and removing adapters from Oxford
+Nanopore reads.  Adapters on the ends of reads are trimmed off, and when a read
+has an adapter in its middle, it is treated as chimeric and chopped into
+separate reads.  Porechop performs thorough alignments to effectively find
+adapters, even at low sequence identity.  Porechop also supports demultiplexing
+of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
+Barcoding Kit or Rapid Barcoding Kit.")
+      (license license:gpl3+))))
+
+(define-public poretools
+  ;; The latest release was in 2016 and the latest commit is from 2017
+  ;; the recommended way to install is to clone the git repository
+  ;; https://poretools.readthedocs.io/en/latest/content/installation.html
+  (let ((commit "e426b1f09e86ac259a00c261c79df91510777407")
+        (revision "1"))
+    (package
+      (name "poretools")
+      (version (git-version "0.6.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/arq5x/poretools.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"))))
+      (build-system python-build-system)
+      ;; requires python >=2.7, <3.0, and the same for python dependencies
+      (arguments `(#:python ,python-2))
+      (inputs
+       `(("hdf5" ,hdf5)))
+      (propagated-inputs
+       `(("python-dateutil" ,python2-dateutil)
+         ("python-h5py" ,python2-h5py)
+         ("python-matplotlib" ,python2-matplotlib)
+         ("python-pandas" ,python2-pandas)
+         ("python-seaborn" ,python2-seaborn)))
+      (home-page "https://poretools.readthedocs.io")
+      (synopsis "Toolkit for working with nanopore sequencing data")
+      (description
+       "The MinION from Oxford Nanopore Technologies is a nanopore sequencer.
+This @code{poretools} package is a flexible toolkit for exploring datasets
+generated by nanopore sequencing devices for the purposes of quality control and
+downstream analysis.  Poretools operates directly on the native FAST5, a variant
+of the Hierarchical Data Format (HDF5) standard.")
+      (license license:expat))))
+
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))