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authorEfraim Flashner2019-08-21 01:37:01 -0500
committerEfraim Flashner2019-08-21 01:37:01 -0500
commitcb7c4cbfa8a1c83ad8cf230d951c0b7913126c1b (patch)
tree2799bac4163ae247e59db5172b8950a82f539b2a
parentdd3831e3c5c3c0f2437e3a6e7f96ced93e3379ab (diff)
downloadguix-bioinformatics-cb7c4cbfa8a1c83ad8cf230d951c0b7913126c1b.tar.gz
gn: edirect-gn: Install missing binary.
* gn/packages/bioinformatics.scm (edirect-gn)[arguments]: Install missing 'efetch' binary. Sort installed files alphabetically. Substitute call to 'exec perl' for all potentially affected files.
-rw-r--r--gn/packages/bioinformatics.scm9
1 files changed, 5 insertions, 4 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 31be859..26337d1 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -943,7 +943,7 @@ reads.")
"rchive.go"
"run-ncbi-converter")
(("gunzip") (string-append gzip "/bin/gunzip")))
- (substitute* "efetch"
+ (substitute* (find-files "." "^e")
(("exec perl") "exec"))
(substitute* '("xtract" "rchive")
;; or add current directory to PATH
@@ -957,9 +957,10 @@ reads.")
(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"))
+ '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed"
+ "edirect.pl" "efetch" "epost" "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"))
(chmod (string-append bin "/xtract.Linux") #o555)