01/01: gnu: f-seq: Fix location of commons-cli.jar.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit c0770feedd08b6e479125dae32c7fe3411adf455
Author: Ricardo Wurmus <address@hidden>
Date:   Wed Oct 18 23:53:18 2017 +0200

    gnu: f-seq: Fix location of commons-cli.jar.
    
    * gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of
    commons-cli.jar in the wrapper script.
---
 gnu/packages/bioinformatics.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32603ae..d15f6fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10035,13 +10035,18 @@ browser.")
          #:phases
          (modify-phases %standard-phases
            (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
+             (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((target (assoc-ref outputs "out"))
                       (doc (string-append target "/share/doc/f-seq/")))
                  (mkdir-p target)
                  (mkdir-p doc)
                  (substitute* "bin/linux/fseq"
-                   (("java") (which "java")))
+                   (("java") (which "java"))
+                   (("\\$REALDIR/../lib/commons-cli-1.1.jar")
+                    (string-append (assoc-ref inputs "java-commons-cli")
+                                   "/share/java/commons-cli.jar"))
+                   (("REALDIR=.*")
+                    (string-append "REALDIR=" target "/bin\n")))
                  (install-file "README.txt" doc)
                  (install-file "bin/linux/fseq" (string-append target "/bin"))
                  (install-file "build~/fseq.jar" (string-append target "/lib"))