Merge branch 'master' into core-updates

1 files changed, 87 insertions, 7 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab9dc185a3..91bb94c549 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11735,19 +11735,39 @@ using nucleotide or amino-acid sequence data.")
 (define-public kallisto
   (package
     (name "kallisto")
-    (version "0.43.1")
+    (version "0.44.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/pachterlab/"
-                                  "kallisto/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pachterlab/kallisto.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
+                "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m"))))
     (build-system cmake-build-system)
-    (arguments `(#:tests? #f))          ; no "check" target
+    (arguments
+     `(#:tests? #f          ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-htslib
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("^ExternalProject_Add" m)
+                (string-append "if (NEVER)\n" m))
+               (("^\\)")
+                (string-append ")\nendif(NEVER)"))
+               (("include_directories\\(\\$\\{htslib_PREFIX.*" m)
+                (string-append "# " m)))
+             (substitute* "src/CMakeLists.txt"
+               (("target_link_libraries\\(kallisto kallisto_core pthread \
+\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)")
+                "target_link_libraries(kallisto kallisto_core pthread hts)")
+               (("include_directories\\(\\.\\./ext/htslib\\)") ""))
+             #t)))))
     (inputs
      `(("hdf5" ,hdf5)
+       ("htslib" ,htslib)
        ("zlib" ,zlib)))
     (home-page "http://pachterlab.github.io/kallisto/")
     (synopsis "Near-optimal RNA-Seq quantification")
@@ -14057,3 +14077,63 @@ absolute GSEA.")
     (description "Ngless is a domain-specific language for
 @dfn{next-generation sequencing} (NGS) data processing.")
     (license license:expat)))
+
+(define-public filtlong
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Filtlong#installation
+  ;; and the lastest release is more than nine months old
+  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
+        (revision "1"))
+    (package
+      (name "filtlong")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Filtlong.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; no check target
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scripts (string-append out "/share/filtlong/scripts")))
+                 (install-file "bin/filtlong" bin)
+                 (install-file "scripts/histogram.py" scripts)
+                 (install-file "scripts/read_info_histograms.sh" scripts))
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (path (getenv "PYTHONPATH")))
+                 (wrap-program (string-append out
+                                              "/share/filtlong/scripts/histogram.py")
+                   `("PYTHONPATH" ":" prefix (,path))))
+               #t))
+           (add-before 'check 'patch-tests
+             (lambda _
+               (substitute* "scripts/read_info_histograms.sh"
+                 (("awk") (which "gawk")))
+               #t)))))
+      (inputs
+       `(("gawk" ,gawk)                 ;for read_info_histograms.sh
+         ("python" ,python-2)           ;required for histogram.py
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/rrwick/Filtlong/")
+      (synopsis "Tool for quality filtering of Nanopore and PacBio data")
+      (description
+       "The Filtlong package is a tool for filtering long reads by quality.
+It can take a set of long reads and produce a smaller, better subset.  It uses
+both read length (longer is better) and read identity (higher is better) when
+choosing which reads pass the filter.")
+      (license (list license:gpl3       ;filtlong
+                     license:asl2.0))))) ;histogram.py