diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 15 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2e31d85b2d..1977fd3bf9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -233,9 +233,8 @@ computational cluster.") 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) (for-each (lambda (file) - (copy-file file (string-append bin (basename file)))) + (install-file file bin)) (find-files "bin" ".*")))) %standard-phases))))) (home-page "https://github.com/arq5x/bedtools2") @@ -559,9 +558,8 @@ confidence to have in an alignment.") 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) (for-each (lambda (file) - (copy-file file (string-append bin file))) + (install-file file bin)) (find-files "." "bowtie2.*")))) (alist-replace 'check @@ -611,9 +609,9 @@ gapped, local, and paired-end alignment modes.") (mkdir-p bin) (mkdir-p doc) (mkdir-p man) - (copy-file "bwa" (string-append bin "/bwa")) - (copy-file "README.md" (string-append doc "/README.md")) - (copy-file "bwa.1" (string-append man "/bwa.1")))) + (install-file "bwa" bin) + (install-file "README.md" doc) + (install-file "bwa.1" man))) ;; no "configure" script (alist-delete 'configure %standard-phases)))) (inputs `(("zlib" ,zlib))) @@ -1308,14 +1306,12 @@ estimates transcript expression.") (alist-replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) - (for-each - (lambda (file) - (copy-file file (string-append bin file))) - (find-files - "." - "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) + (let ((bin (string-append (assoc-ref outputs "out") "/bi/"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files + "." + "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) (alist-delete 'configure %standard-phases))))) (native-inputs `(("unzip" ,unzip))) @@ -2091,17 +2087,14 @@ distribution, coverage uniformity, strand specificity, etc.") 'install 'install-library (lambda* (#:key outputs #:allow-other-keys) (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (mkdir-p lib) - (copy-file "libbam.a" (string-append lib "/libbam.a")))) + (install-file "libbam.a" lib))) (alist-cons-after 'install 'install-headers (lambda* (#:key outputs #:allow-other-keys) (let ((include (string-append (assoc-ref outputs "out") "/include/samtools/"))) - (mkdir-p include) (for-each (lambda (file) - (copy-file file (string-append include - (basename file)))) + (install-file file include)) (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)) (alist-delete 'configure %standard-phases)))))) @@ -2356,8 +2349,7 @@ accessed/downloaded on demand across HTTP.") (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) - (copy-file "plink" (string-append bin "plink")) + (install-file "plink" bin) #t)))))) (inputs `(("zlib" ,zlib) @@ -2579,8 +2571,7 @@ bioinformatics file formats, sequence alignment, and more.") 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) - (copy-file "STAR" (string-append bin "STAR")))) + (install-file "STAR" bin))) (alist-delete 'configure %standard-phases))))) (native-inputs |