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authorEfraim Flashner2020-02-16 04:56:41 -0600
committerEfraim Flashner2020-02-16 04:56:41 -0600
commitbc065d21f3add434a4c5958ffe93383c2d848795 (patch)
treede15ae73fbff09cd814f20c17a39148654dbdc88 /gn
parent0460e93f0832ed10316eed05a4d6f2ceb5b61922 (diff)
downloadguix-bioinformatics-bc065d21f3add434a4c5958ffe93383c2d848795.tar.gz
gn: edirect-gn: Wrap more binaries
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm30
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)