diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 31 |
1 files changed, 20 insertions, 11 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 66d4d2d..4cb8c7c 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -426,6 +426,15 @@ reads.") ; (lambda* (#:key inputs #:allow-other-keys) ; (let ((go (string-append (assoc-ref inputs "go") "/bin/go"))) ; (invoke go "build" "xtract.go")))) + (add-after 'unpack 'unpack-binaries + (lambda* (#:key inputs #:allow-other-keys) + (let ((gzip (assoc-ref inputs "gzip")) + (xtract (assoc-ref inputs "xtract.Linux")) + (rchive (assoc-ref inputs "rchive.Linux"))) + (copy-file xtract "xtract.Linux.gz") + (copy-file rchive "rchive.Linux.gz") + (invoke (string-append gzip "/bin/gzip") "xtract.Linux.gz" "-dfv") + (invoke (string-append gzip "/bin/gzip") "rchive.Linux.gz" "-dfv")))) (add-after 'unpack 'patch-programs (lambda _ (substitute* (find-files "." "^e") @@ -435,10 +444,8 @@ reads.") ((".*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"))) + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (for-each (lambda (file) (install-file file bin)) @@ -446,8 +453,8 @@ reads.") "edirect.pl" "efetch" "epost" "esearch" "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" "pm-stash" "rchive" "xtract")) - (copy-file xtract.linux (string-append bin "/xtract.Linux")) - (copy-file rchive.linux (string-append bin "/rchive.Linux")) + (install-file "xtract.Linux" bin) + (install-file "rchive.Linux" bin) (chmod (string-append bin "/xtract.Linux") #o555) (chmod (string-append bin "/rchive.Linux") #o555)) #t)) @@ -475,19 +482,21 @@ reads.") ("xtract.Linux" ,(origin (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "/xtract.Linux")) ;; March 10, 2016 + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" + "/versions/" (package-version edirect) + "/xtract.Linux.gz")) (sha256 (base32 - "15yhhh8kfipk12rhzabap81ys8wgj0khn0mp8p7zwqhq028fwj0l")))) + "1idzynn446qqjx2wv4jjgsx6cp349d4jy8g9z4gsg9l6sn5dhx53")))) ("rchive.Linux" ,(origin (method url-fetch) (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "/rchive.Linux")) ;; November 14, 2017 + "/versions/" (package-version edirect) + "/rchive.Linux.gz")) (sha256 (base32 - "0hl8zj1md9xbmaj0pv99rjyisw8w74rirw97xwqk47dz8v8ml338")))))) + "1p65hifv5d6nxg01vjwgy2nw49nssd822a8aj8jv412mhzj95ihv")))))) (native-search-paths ;; Ideally this should be set for LWP somewhere. (list (search-path-specification |