gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.

* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
  plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
  Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.

gnu/packages/bioinformatics.scm

@@ -228,9 +228,8 @@ 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")
@@ -554,9 +553,8 @@ 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
@@ -606,9 +604,9 @@ 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)))
@@ -1264,14 +1262,12 @@ 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)))
@@ -1989,17 +1985,14 @@ 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))))))
@@ -2254,8 +2247,7 @@ 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)
@@ -2477,8 +2469,7 @@ 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

gnu/packages/check.scm

@@ -136,10 +136,9 @@ supervised tests.")
                                                  ,version)))
                      (begin
                        (for-each mkdir-p (list incdir docdir))
-                       (copy-file (string-append source
+                       (install-file (string-append source
                                                  "/single_include/catch.hpp")
-                                  (string-append incdir
-                                                 "/catch.hpp"))
+                                     incdir)
                        (copy-recursively (string-append source "/docs")
                                          docdir))))))
     (home-page "http://catch-lib.net/")

gnu/packages/code.scm

@@ -117,9 +117,8 @@ highlighting your own code that seemed comprehensible when you wrote it.")
                    (let* ((out  (assoc-ref outputs "out"))
                           (data (string-append out "/share/gtags"))
                           (lisp (string-append out "/share/emacs/site-lisp")))
-                     (mkdir-p lisp)
-                     (copy-file (string-append data "/gtags.el")
-                                (string-append lisp "/gtags.el"))
+                     (install-file (string-append data "/gtags.el")
+                                   lisp)
                      (delete-file (string-append data "/gtags.el"))
                      #t))
                  %standard-phases)))

gnu/packages/emacs.scm

@@ -406,9 +406,9 @@ operations.")
                 (lisp-dir (string-append %output "/share/emacs/site-lisp")))
            (setenv "PATH" PATH)
            (system* tar "xvf" source)
-           (mkdir-p lisp-dir)
-           (copy-file (string-append ,name "-" ,version "/magit-svn.el")
-                      (string-append lisp-dir "/magit-svn.el"))
+
+           (install-file (string-append ,name "-" ,version "/magit-svn.el")
+                         lisp-dir)
 
            (with-directory-excursion lisp-dir
              (parameterize ((%emacs emacs))
@@ -462,18 +462,14 @@ support for Git-SVN.")
                          out "/share/doc/haskell-mode-" ,version))
                    (info (string-append out "/share/info")))
               (define (copy-to-dir dir files)
-                (mkdir-p dir)
-                (for-each
-                 (lambda (f)
-                   (copy-file f (string-append dir "/" (basename f))))
-                 files))
+                (for-each (lambda (f)
+                            (install-file f dir))
+                          files))
 
               (with-directory-excursion "doc"
                 (unless (zero? (system* "makeinfo" "haskell-mode.texi"))
                   (error "makeinfo failed"))
-                (mkdir-p info)
-                (copy-file "haskell-mode.info"
-                           (string-append info "/haskell-mode.info")))
+                (install-file "haskell-mode.info" info))
                (copy-to-dir doc '("CONTRIBUTING.md" "NEWS" "README.md"))
                (copy-to-dir el-dir (find-files "." "\\.elc?"))
                ;; these are now distributed with emacs
@@ -876,11 +872,9 @@ single buffer.")
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((target (string-append (assoc-ref outputs "out")
                                          "/share/emacs/site-lisp/")))
-              (mkdir-p target)
-              (for-each
-               (lambda (file)
-                 (copy-file file (string-append target (basename file))))
-               (find-files "../lisp" "^(pdf|tab).*\\.elc?"))
+              (for-each (lambda (file)
+                          (install-file file target))
+                        (find-files "../lisp" "^(pdf|tab).*\\.elc?"))
               (emacs-byte-compile-directory target)
               (emacs-generate-autoloads "pdf-tools" target)))))))
     (native-inputs `(("autoconf" ,autoconf)

gnu/packages/engineering.scm

@@ -300,11 +300,9 @@ optimizer; and it can produce photorealistic and design review images.")
                            (doc (string-append data "/doc/" ,name "-" ,version))
                            (examples (string-append doc "/examples")))
                       (with-directory-excursion "bin"
-                        (mkdir-p bin)
-                        (for-each
-                         (lambda (f)
-                           (copy-file f (string-append bin "/" (basename f))))
-                         (find-files "." ".*")))
+                        (for-each (lambda (f)
+                                    (install-file f bin))
+                                  (find-files "." ".*")))
                       (copy-recursively "doc" doc)
                       (copy-recursively "examples" examples)
                       #t))))))
@@ -350,11 +348,9 @@ multipole-accelerated algorithm.")
                            (doc (string-append data "/doc/" ,name "-" ,version))
                            (examples (string-append doc "/examples")))
                       (with-directory-excursion "bin"
-                        (mkdir-p bin)
-                        (for-each
-                         (lambda (f)
-                           (copy-file f (string-append bin "/" (basename f))))
-                         (find-files "." ".*")))
+                        (for-each (lambda (f)
+                                    (install-file f bin))
+                                  (find-files "." ".*")))
                       (copy-recursively "doc" doc)
                       (copy-recursively "examples" examples)
                       #t))))))

gnu/packages/gnuzilla.scm

@@ -190,14 +190,12 @@ in the Mozilla clients.")
                    (obj (match (scandir "dist" (cut string-suffix? "OBJ" <>))
                           ((obj) (string-append "dist/" obj)))))
               ;; Install nss-config to $out/bin.
-              (mkdir-p (string-append out "/bin"))
-              (copy-file (string-append obj "/bin/nss-config")
-                         (string-append out "/bin/nss-config"))
+              (install-file (string-append obj "/bin/nss-config")
+                            (string-append out "/bin"))
               (delete-file (string-append obj "/bin/nss-config"))
               ;; Install nss.pc to $out/lib/pkgconfig.
-              (mkdir-p (string-append out "/lib/pkgconfig"))
-              (copy-file (string-append obj "/lib/pkgconfig/nss.pc")
-                         (string-append out "/lib/pkgconfig/nss.pc"))
+              (install-file (string-append obj "/lib/pkgconfig/nss.pc")
+                            (string-append out "/lib/pkgconfig"))
               (delete-file (string-append obj "/lib/pkgconfig/nss.pc"))
               (rmdir (string-append obj "/lib/pkgconfig"))
               ;; Install other files.

gnu/packages/guile.scm

@@ -452,7 +452,7 @@ http:://json.org specification.  These are the main features:
                      scm-files)
 
            ;; Also copy over the README.
-           (copy-file "README.org" (string-append doc "/README.org"))
+           (install-file "README.org" doc)
            #t))))
     (inputs
      `(("guile" ,guile-2.0)))

gnu/packages/java.scm

@@ -102,8 +102,8 @@
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((java (string-append (assoc-ref outputs "out")
                                        "/share/java")))
-              (mkdir-p java)
-              (copy-file "swt.jar" (string-append java "/swt.jar"))) #t)
+              (install-file "swt.jar" java)
+              #t))
           (alist-delete 'configure %standard-phases))))))
     (inputs
      `(("xulrunner" ,icecat)

gnu/packages/make-bootstrap.scm

@@ -253,10 +253,8 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
 
             ;; But of course, there are exceptions to this rule.
             (let ((grep (assoc-ref %build-inputs "grep")))
-              (copy-file (string-append grep "/bin/fgrep")
-                         (string-append bin "/fgrep"))
-              (copy-file (string-append grep "/bin/egrep")
-                         (string-append bin "/egrep")))
+              (install-file (string-append grep "/bin/fgrep") bin)
+              (install-file (string-append grep "/bin/egrep") bin))
 
             ;; Clear references to the store path.
             (for-each remove-store-references

gnu/packages/maths.scm

@@ -1828,21 +1828,17 @@ specifications.")
                           (string-append lib "/liblpsolve55.a"))
                (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
                           (string-append lib "/liblpsolve55.so"))
-               (mkdir-p bin)
-               (copy-file "lp_solve/bin/ux64/lp_solve"
-                          (string-append bin "/lp_solve"))
-               (mkdir-p include)
+               (install-file "lp_solve/bin/ux64/lp_solve" bin)
+
                ;; Install a subset of the header files as on Debian
                ;; (plus lp_bit.h, which matches the regular expression).
-               (for-each
-                 (lambda (name)
-                   (copy-file name (string-append include "/" name)))
-                 (find-files "." "lp_[HMSa-z].*\\.h$"))
+               (for-each (lambda (name)
+                           (install-file name include))
+                         (find-files "." "lp_[HMSa-z].*\\.h$"))
                (with-directory-excursion "shared"
-                 (for-each
-                   (lambda (name)
-                     (copy-file name (string-append include "/" name)))
-                   (find-files "." "\\.h$")))
+                 (for-each (lambda (name)
+                             (install-file name include))
+                           (find-files "." "\\.h$")))
                #t))))))
     (home-page "http://lpsolve.sourceforge.net/")
     (synopsis "Mixed integer linear programming (MILP) solver")

gnu/packages/mp3.scm

@@ -435,7 +435,7 @@ format.")
                     (let* ((out (assoc-ref outputs "out"))
                            (bin (string-append out "/bin")))
                       (mkdir-p bin)
-                      (copy-file "mpc123" (string-append bin "/mpc123"))))
+                      (install-file "mpc123" bin)))
                   %standard-phases))
        #:tests? #f))
 

gnu/packages/ninja.scm

@@ -66,11 +66,8 @@
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (doc (string-append out "/share/doc/ninja")))
-              (mkdir-p bin)
-              (copy-file "ninja" (string-append bin "/ninja"))
-              (mkdir-p doc)
-              (copy-file "doc/manual.asciidoc"
-                         (string-append doc "/manual.asciidoc"))
+              (install-file "ninja" bin)
+              (install-file "doc/manual.asciidoc" doc)
               #t))))))
     (home-page "http://martine.github.io/ninja/")
     (synopsis "Small build system")

gnu/packages/python.scm

@@ -2784,7 +2784,7 @@ association studies (GWAS) on extremely large data sets.")
                                          (tgt-dir (string-append html "/" dir)))
                                     (unless (equal? "." dir)
                                       (mkdir-p tgt-dir))
-                                    (copy-file file (string-append html "/" file))))
+                                    (install-file file html)))
                                 (find-files "." ".*"))))))
               ,phases)))))))
 
@@ -2828,7 +2828,7 @@ association studies (GWAS) on extremely large data sets.")
             (for-each
              (lambda (dir tgt)
                (map (lambda (file)
-                      (copy-file file (string-append tgt "/" (basename file))))
+                      (install-file file tgt))
                     (find-files dir ".*")))
              (list "docs" "htmldoc" "examples")
              (list doc html-doc examples))))
@@ -3140,9 +3140,7 @@ atlas_libs = openblas
                  (for-each (lambda (file)
                              (let* ((dir (dirname file))
                                     (tgt-dir (string-append html "/" dir)))
-                               (unless (equal? "." dir)
-                                 (mkdir-p tgt-dir))
-                               (copy-file file (string-append html "/" file))))
+                               (install-file file html)))
                            (find-files "." ".*"))))))
          ;; Tests can only be run after the library has been installed and not
          ;; within the source directory.

gnu/packages/screen.scm

@@ -79,8 +79,7 @@ view to show two terminals at once.")
                  'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((out (assoc-ref outputs "out")))
-                     (mkdir-p (string-append out "/bin"))
-                     (copy-file "dtach" (string-append out "/bin/dtach"))))
+                     (install-file "dtach" (string-append out "/bin"))))
                  %standard-phases)
        ;; No check target.
        #:tests? #f))

gnu/packages/synergy.scm

@@ -92,19 +92,15 @@
                      (ex  (string-append out "/share/doc/synergy-"
                                          ,version "/examples")))
                 (begin
-                  (mkdir-p bin)
                   (for-each
                    (lambda (f)
-                     (copy-file (string-append srcdir "/bin/" f)
-                                (string-append bin "/" f)))
+                     (install-file (string-append srcdir "/bin/" f) bin))
                    '("synergyc" "synergys" "synergyd"
                      "usynergy" "syntool"))
                   ;; Install example configuration files
-                  (mkdir-p ex)
                   (for-each
                    (lambda (e)
-                     (copy-file (string-append srcdir "/doc/" e)
-                                (string-append ex "/" e)))
+                     (install-file (string-append srcdir "/doc/" e) ex))
                    '("synergy.conf.example"
                      "synergy.conf.example-advanced"
                      "synergy.conf.example-basic")))))

gnu/packages/textutils.scm

@@ -111,11 +111,9 @@ libenca and several charset conversion libraries and tools.")
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((lib (string-append (assoc-ref outputs "out") "/lib/"))
                 (include (string-append (assoc-ref outputs "out") "/include/")))
-            (mkdir-p lib)
-            (mkdir-p include)
-            (copy-file "utf8proc.h" (string-append include "utf8proc.h"))
+            (install-file "utf8proc.h" include)
             (for-each (lambda (file)
-                        (copy-file file (string-append lib (basename file))))
+                        (install-file file lib))
                       '("libutf8proc.a" "libutf8proc.so"))))
         ;; no configure script
         (alist-delete 'configure %standard-phases))))

gnu/packages/version-control.scm

@@ -432,11 +432,9 @@ lot easier.")
                             (output (assoc-ref %outputs "out"))
                             (bindir (string-append output "/bin"))
                             (script "git-test-sequence"))
-                       (begin
-                         (mkdir-p bindir)
-                         (copy-file (string-append source "/" script)
-                                    (string-append bindir "/" script))
-                         #t)))))
+                       (install-file (string-append source "/" script)
+                                     bindir)
+                       #t))))
       (home-page "http://dustin.sallings.org/2010/03/28/git-test-sequence.html")
       (synopsis "Run a command over a sequence of commits")
       (description

gnu/packages/wicd.scm

@@ -174,16 +174,13 @@
              ;; directory.
              (let ((dest-dir (string-append out "/etc/wicd"))
                    (name "dhclient.conf.template.default"))
-               (mkdir-p dest-dir)
-               (copy-file (string-append "other/" name)
-                          (string-append dest-dir "/" name)))
+               (install-file (string-append "other/" name) dest-dir))
 
              ;; Copy index.theme from hicolor-icon-theme.  This is needed to
              ;; allow wicd-gtk to find its icons.
              (let ((hicolor (assoc-ref inputs "hicolor-icon-theme"))
                    (name "/share/icons/hicolor/index.theme"))
-               (copy-file (string-append hicolor name)
-                          (string-append out name)))
+               (install-file (string-append hicolor name) out))
              #t))
          %standard-phases))))
     (synopsis "Network connection manager")