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branch master updated: gnu: kraken2: Replace references to rsync.
From: |
guix-commits |
Subject: |
branch master updated: gnu: kraken2: Replace references to rsync. |
Date: |
Wed, 28 Apr 2021 08:51:10 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new f01b3cd gnu: kraken2: Replace references to rsync.
f01b3cd is described below
commit f01b3cd0632d3ef7e609625e0dd32028a5c930d7
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Apr 28 14:48:39 2021 +0200
gnu: kraken2: Replace references to rsync.
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
---
gnu/packages/bioinformatics.scm | 85 +++++++++++++++++++++++------------------
1 file changed, 47 insertions(+), 38 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 97f3f91..92c0692 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -130,6 +130,7 @@
#:use-module (gnu packages qt)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages rsync)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
@@ -15182,50 +15183,58 @@ international community.")
(add-before 'install 'install-scripts
(lambda* (#:key outputs #:allow-other-keys)
(let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
- (scripts (find-files "scripts" ".*"))
(replacements `(("KRAKEN2_DIR" . ,bin)
("VERSION" . ,,version))))
(mkdir-p bin)
- (substitute* scripts
- (("#####=([^=]+)=#####" _ key)
- (or (assoc-ref replacements key)
- (error (format #false "unknown key: ~a~%" key)))))
- (substitute* "scripts/kraken2"
- (("compression_program = \"bzip2\"")
- (string-append "compression_program = \""
- (which "bzip2")
- "\""))
- (("compression_program = \"gzip\"")
- (string-append "compression_program = \""
- (which "gzip")
- "\"")))
- (substitute* '("scripts/download_genomic_library.sh"
- "scripts/download_taxonomy.sh"
- "scripts/16S_gg_installation.sh"
- "scripts/16S_silva_installation.sh"
- "scripts/16S_rdp_installation.sh")
- (("wget") (which "wget")))
- (substitute* "scripts/mask_low_complexity.sh"
- (("which") (which "which")))
- (substitute* '("scripts/mask_low_complexity.sh"
- "scripts/download_genomic_library.sh"
- "scripts/16S_silva_installation.sh")
- (("sed -e ")
- (string-append (which "sed") " -e ")))
- (substitute* '("scripts/rsync_from_ncbi.pl"
- "scripts/16S_rdp_installation.sh"
- "scripts/16S_silva_installation.sh"
- "scripts/16S_gg_installation.sh"
- "scripts/download_taxonomy.sh"
- "scripts/download_genomic_library.sh")
- (("gunzip") (which "gunzip")))
- (for-each (lambda (script)
- (chmod script #o555)
- (install-file script bin))
- scripts)))))))
+
+ (with-directory-excursion "scripts"
+ (let ((scripts (find-files "." ".*")))
+ (substitute* scripts
+ (("#####=([^=]+)=#####" _ key)
+ (or (assoc-ref replacements key)
+ (error (format #false "unknown key: ~a~%" key)))))
+ (substitute* "kraken2"
+ (("compression_program = \"bzip2\"")
+ (string-append "compression_program = \""
+ (which "bzip2")
+ "\""))
+ (("compression_program = \"gzip\"")
+ (string-append "compression_program = \""
+ (which "gzip")
+ "\"")))
+ (substitute* '("download_genomic_library.sh"
+ "download_taxonomy.sh"
+ "16S_gg_installation.sh"
+ "16S_silva_installation.sh"
+ "16S_rdp_installation.sh")
+ (("wget") (which "wget")))
+ (substitute* '("download_taxonomy.sh"
+ "download_genomic_library.sh"
+ "rsync_from_ncbi.pl")
+ (("rsync -")
+ (string-append (which "rsync") " -")))
+ (substitute* "mask_low_complexity.sh"
+ (("which") (which "which")))
+ (substitute* '("mask_low_complexity.sh"
+ "download_genomic_library.sh"
+ "16S_silva_installation.sh")
+ (("sed -e ")
+ (string-append (which "sed") " -e ")))
+ (substitute* '("rsync_from_ncbi.pl"
+ "16S_rdp_installation.sh"
+ "16S_silva_installation.sh"
+ "16S_gg_installation.sh"
+ "download_taxonomy.sh"
+ "download_genomic_library.sh")
+ (("gunzip") (which "gunzip")))
+ (for-each (lambda (script)
+ (chmod script #o555)
+ (install-file script bin))
+ scripts)))))))))
(inputs
`(("gzip" ,gzip)
("perl" ,perl)
+ ("rsync" ,rsync)
("sed" ,sed)
("wget" ,wget)
("which" ,which)))
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