From dce1ae9dbfe7c33dcac7f64682eb9368b6480b6d Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 18 Feb 2020 13:32:09 +0200
Subject: gn: Update edirect-gn to match upstream update.
---
gn/packages/bioinformatics.scm | 31 ++++++++++++++++++++-----------
1 file 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
--
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