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gnu: kraken2: Replace references to rsync.

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* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
This commit is contained in:
Ricardo Wurmus 2021-04-28 14:48:39 +02:00
parent f7ff886213
commit f01b3cd063
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GPG key ID: 197A5888235FACAC
1 changed files with 47 additions and 38 deletions
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85
gnu/packages/bioinformatics.scm
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@ -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)))