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-rw-r--r--gnu/packages/bioinformatics.scm39
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