diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 91 |
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"))) |