diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 30 |
1 files changed, 13 insertions, 17 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 8897752..66d4d2d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -427,20 +427,12 @@ reads.") ; (let ((go (string-append (assoc-ref inputs "go") "/bin/go"))) ; (invoke go "build" "xtract.go")))) (add-after 'unpack 'patch-programs - (lambda* (#:key inputs #:allow-other-keys) - (let ((gzip (assoc-ref inputs "gzip"))) - (substitute* '("index-bioc" - "pm-index" - "pm-invert" - "pm-stash" - "rchive.go" - "run-ncbi-converter") - (("gunzip") (string-append gzip "/bin/gunzip"))) - (substitute* (find-files "." "^e") - (("exec perl") "exec")) - (substitute* '("xtract" "rchive") - ;; or add current directory to PATH - ((".*PATH.*") ""))) + (lambda _ + (substitute* (find-files "." "^e") + (("exec perl") "exec")) + (substitute* '("xtract" "rchive") + ;; or add current directory to PATH + ((".*PATH.*") "")) #t)) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) @@ -466,9 +458,13 @@ reads.") (path (getenv "PERL5LIB"))) (for-each (lambda (file) - (wrap-program (string-append out "/bin/" file) - `("PERL5LIB" ":" prefix (,path)))) - '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls"))) + (wrap-program file + `("PERL5LIB" ":" prefix (,path))) + (wrap-program file + `("PATH" ":" prefix (,(dirname (which "sed")) + ,(dirname (which "gzip")) + ,(dirname (which "uname")))))) + (find-files out "."))) #t)))))) (inputs `(("gzip" ,gzip) |