diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf8eb2e697..e2590787ad 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4470,6 +4470,7 @@ distribution, coverage uniformity, strand specificity, etc.")
                 (uri (hg-reference
                       (url "https://bitbucket.org/libsleipnir/sleipnir")
                       (changeset changeset)))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
@@ -4488,6 +4489,9 @@ distribution, coverage uniformity, strand specificity, etc.")
            (modify-phases %standard-phases
              (add-after 'unpack 'bootstrap
                (lambda _
+                 ;; first we have to patch a shebang
+                 (substitute* "gen_tools_am"
+                   (("/usr/bin/env perl") (which perl)))
                  (zero? (system* "bash" "gen_auto"))))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)