01/02: gnu: khmer: Make gzip timestamps writable.

[guix-commits]

efraim pushed a commit to branch master
in repository guix.

commit d9340de9031211c220b5b710e64af29e066f26f2
Author: Brian Leung <address@hidden>
Date:   Tue Jun 25 20:48:54 2019 +0200

    gnu: khmer: Make gzip timestamps writable.
    
    * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase
    to make gzip timestamps writable.
    
    Signed-off-by: Efraim Flashner <address@hidden>
---
 gnu/packages/bioinformatics.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 89f1ac3..bcec9cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Gábor Boskovits <address@hidden>
 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <address@hidden>
 ;;; Copyright © 2019 Maxim Cournoyer <address@hidden>
+;;; Copyright © 2019 Brian Leung <address@hidden>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4206,8 +4207,15 @@ command, or queried for specific k-mers with 
@code{jellyfish query}.")
        (modify-phases %standard-phases
          (add-after 'unpack 'set-cc
            (lambda _ (setenv "CC" "gcc") #t))
-         ;; FIXME: This fails with "permission denied".
-         (delete 'reset-gzip-timestamps))))
+
+         (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))))))
     (native-inputs
      `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)