diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 85 |
1 files changed, 47 insertions, 38 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97f3f916c8..92c0692f45 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))) |