From 9dc50c8c4742811cb2ca953e075e0ea6e0c09213 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 19 May 2020 12:39:22 +0200
Subject: [PATCH] gnu: sra-tools: Update to 2.10.6.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ad08b9db5..a738aa51a8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6148,7 +6148,7 @@ (define-public python2-screed
 (define-public sra-tools
   (package
     (name "sra-tools")
-    (version "2.9.6")
+    (version "2.10.6")
     (source
      (origin
        (method git-fetch)
@@ -6158,11 +6158,11 @@ (define-public sra-tools
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy"))))
+         "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:parallel-build? #f ; not supported
-       #:tests? #f ; no "check" target
+     `(#:parallel-build? #f             ; not supported
+       #:tests? #f                      ; no "check" target
        #:make-flags
        (list (string-append "DEFAULT_CRT="
                             (assoc-ref %build-inputs "ncbi-vdb")
@@ -6205,6 +6205,9 @@ (define-public sra-tools
              ;; Dynamic linking
              (substitute* "tools/copycat/Makefile"
                (("smagic-static") "lmagic"))
+             (substitute* "tools/driver-tool/utf8proc/Makefile"
+               (("CC\\?=gcc") "myCC=gcc")
+               (("\\(CC\\)") "(myCC)"))
 
              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
@@ -6217,8 +6220,9 @@ (define-public sra-tools
                      (string-append "--with-magic-prefix="
                                     (assoc-ref inputs "libmagic"))
                      ;; TODO: building with libxml2 fails with linker errors
-                     ;; (string-append "--with-xml2-prefix="
-                     ;;                (assoc-ref inputs "libxml2"))
+                     #;
+                     (string-append "--with-xml2-prefix="
+                                    (assoc-ref inputs "libxml2"))
                      (string-append "--with-ncbi-vdb-sources="
                                     (assoc-ref inputs "ncbi-vdb"))
                      (string-append "--with-ncbi-vdb-build="
@@ -6234,8 +6238,9 @@ (define-public sra-tools
        ("ncbi-vdb" ,ncbi-vdb)
        ("libmagic" ,file)
        ("fuse" ,fuse)
-       ("hdf5" ,hdf5)
-       ("zlib" ,zlib)))
+       ("hdf5" ,hdf5-1.10)
+       ("zlib" ,zlib)
+       ("python" ,python-wrapper)))
     (home-page
      "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
     (synopsis "Tools and libraries for reading and writing sequencing data")