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-rw-r--r--gnu/packages/bioinformatics.scm9
1 files changed, 7 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32603ae57e..d15f6fd559 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"))