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-rw-r--r--gn/packages/bioinformatics.scm91
1 files changed, 79 insertions, 12 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b7db927..31be859 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -921,17 +921,84 @@ reads.")
;; non-profit/not-for-profit institutions
(license license:non-copyleft)))
-(define-public edirect-11
+(define-public edirect-gn
(package
(inherit edirect)
- (name "edirect")
- (version "11.8.20190730")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
- "/versions/" version
- "/edirect-" version ".tar.gz"))
- (sha256
- (base32
- "037sn5qmari98z5pmmrf9zx3il017nfp67p5hvq1pqzxhv6i29l3"))))))
+ (name "edirect-gn")
+ (arguments
+ (substitute-keyword-arguments (package-arguments edirect)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ ; (replace 'build
+ ; (lambda* (#:key inputs #:allow-other-keys)
+ ; (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* "efetch"
+ (("exec perl") "exec"))
+ (substitute* '("xtract" "rchive")
+ ;; or add current directory to PATH
+ ((".*PATH.*") "")))
+ #t))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (xtract.linux (assoc-ref inputs "xtract.Linux"))
+ (rchive.linux (assoc-ref inputs "rchive.Linux")))
+ (for-each
+ (lambda (file)
+ (install-file file bin))
+ '("edirect.pl" "archive-pubmed" "pm-prepare" "download-pubmed"
+ "pm-stash" "pm-refresh" "fetch-pubmed" "xtract" "has-asp"
+ "asp-ls" "asp-cp" "ftp-ls" "ftp-cp" "rchive" "efetch"))
+ (copy-file xtract.linux (string-append bin "/xtract.Linux"))
+ (copy-file rchive.linux (string-append bin "/rchive.Linux"))
+ (chmod (string-append bin "/xtract.Linux") #o555)
+ (chmod (string-append bin "/rchive.Linux") #o555))
+ #t))
+ (replace 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+ (let ((out (assoc-ref outputs "out"))
+ (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")))
+ #t))))))
+ (inputs
+ `(("gzip" ,gzip)
+ ,@(package-inputs edirect)))
+ (native-inputs
+ `(
+ ;("go" ,go)
+ ("xtract.Linux"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
+ "versions/" (package-version edirect) "/xtract.Linux"))
+ (file-name (string-append "xtract.Linux-" (package-version edirect)))
+ (sha256
+ (base32
+ "0fx6arpn38spnwszmvkkpa3498qrrlglg2l9jw91icgqbyjjq9wq"))))
+ ("rchive.Linux"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
+ "versions/" (package-version edirect) "/rchive.Linux"))
+ (file-name (string-append "rchive.Linux-" (package-version edirect)))
+ (sha256
+ (base32
+ "134y0zprplqlplc6qmcjb97411bxkwghmq3z0qjgh0dgdbzjq1w3"))))))
+ ;; Due to the precompiled binaries we download:
+ (supported-systems "x86_64-linux")))