03/06: gnu: Use INSTALL-FILE where appropriate.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit f38607536e10f8991bf67d4f6dc5e0632f206f47
Author: Tobias Geerinckx-Rice <address@hidden>
Date:   Mon Mar 13 16:19:06 2017 +0100

    gnu: Use INSTALL-FILE where appropriate.
    
    * gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
    INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
    * gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
    edirect, fasttree, rsem, samtools-0.1): Likewise.
    * gnu/packages/code.scm (withershins): Likewise.
    * gnu/packages/conky.scm (conky): Likewise.
    * gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
    * gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
    * gnu/packages/engineering.scm (librecad): Likewise.
---
 gnu/packages/admin.scm          |  4 +---
 gnu/packages/bioinformatics.scm | 37 ++++++++++++++-----------------------
 gnu/packages/code.scm           | 14 +++++++-------
 gnu/packages/conky.scm          |  2 +-
 gnu/packages/debug.scm          | 14 +++++++-------
 gnu/packages/emacs.scm          |  2 +-
 gnu/packages/engineering.scm    | 14 +++++++-------
 7 files changed, 38 insertions(+), 49 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 4b14e0e..4197f63 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -905,9 +905,7 @@ commands and their arguments.")
                            (man8 (string-append man "/man8")))
                       (define (copy-man-page target)
                         (lambda (file)
-                          (copy-file file
-                                     (string-append target "/"
-                                                    (basename file)))))
+                          (install-file file target)))
 
                       (mkdir-p man5) (mkdir man8)
                       (for-each (copy-man-page man5)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 239b94b..3387a25 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -151,11 +151,9 @@ and several other tools.")
                            (bin (string-append out "/bin"))
                            (man (string-append out "/share/man/man1")))
                       (mkdir-p bin)
-                      (copy-file "aragorn"
-                                 (string-append bin "/aragorn"))
+                      (install-file "aragorn" bin)
                       (mkdir-p man)
-                      (copy-file "aragorn.1"
-                                 (string-append man "/aragorn.1")))
+                      (install-file "aragorn.1" man))
                     #t)))))
     (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN";)
     (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
@@ -1700,15 +1698,16 @@ gene predictor designed to work with assembled, aligned 
RNA-seq transcripts.")
          (replace
           'install
           (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
+            (let* ((out (assoc-ref outputs "out"))
+                   (bin (string-append out "/bin")))
               (copy-recursively "src" (string-append out "/src"))
-              (mkdir (string-append out "/bin"))
+              (mkdir bin)
               ;; Add "src" directory to module lookup path.
               (substitute* "couger"
                 (("from argparse")
                  (string-append "import sys\nsys.path.append(\""
                                 out "\")\nfrom argparse")))
-              (copy-file "couger" (string-append out "/bin/couger")))
+              (install-file "couger" bin))
             #t))
          (add-after
           'install 'wrap-program
@@ -2231,8 +2230,7 @@ quantitative phenotypes.")
                     (let ((target (string-append (assoc-ref outputs "out")
                                                  "/bin")))
                       (mkdir-p target)
-                      (copy-file "edirect.pl"
-                                 (string-append target "/edirect.pl"))
+                      (install-file "edirect.pl" target)
                       #t)))
          (add-after
           'install 'wrap-program
@@ -2378,10 +2376,8 @@ ChIP-Seq, and analysis of metagenomic data.")
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin")))
                      (mkdir-p bin)
-                     (copy-file "scripts/convertToEBD.py"
-                                (string-append bin "/convertToEBD.py"))
-                     (copy-file "bin/ExpressBetaDiversity"
-                                (string-append bin "/ExpressBetaDiversity"))
+                     (install-file "scripts/convertToEBD.py" bin)
+                     (install-file "bin/ExpressBetaDiversity" bin)
                      #t))))))
    (inputs
     `(("python" ,python-2)))
@@ -2440,10 +2436,8 @@ similarity of community members.")
             (let ((bin (string-append (assoc-ref outputs "out")
                                       "/bin")))
               (mkdir-p bin)
-              (copy-file "FastTree"
-                         (string-append bin "/FastTree"))
-              (copy-file "FastTreeMP"
-                         (string-append bin "/FastTreeMP"))
+              (install-file "FastTree" bin)
+              (install-file "FastTreeMP" bin)
               #t))))))
    (home-page "http://www.microbesonline.org/fasttree";)
    (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
@@ -4101,11 +4095,9 @@ phylogenies.")
                       (mkdir-p bin)
                       (mkdir-p perl)
                       (for-each (lambda (file)
-                                  (copy-file file
-                                             (string-append bin (basename 
file))))
+                                  (install-file file bin))
                                 (find-files "." "rsem-.*"))
-                      (copy-file "rsem_perl_utils.pm"
-                                 (string-append perl "/rsem_perl_utils.pm")))
+                      (install-file "rsem_perl_utils.pm" perl))
                     #t))
          (add-after
           'install 'wrap-program
@@ -4336,8 +4328,7 @@ viewer.")
                    (let ((bin (string-append
                                (assoc-ref outputs "out") "/bin")))
                      (mkdir-p bin)
-                     (copy-file "samtools"
-                                (string-append bin "/samtools"))
+                     (install-file "samtools" bin)
                      #t)))
                (delete 'patch-tests)
                (delete 'configure))))))))
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index f91fdab..3aaa754 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -271,13 +271,13 @@ features that are not supported by the standard 
@code{stdio} implementation.")
          (replace
           'install
           (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
-              (mkdir-p (string-append out "/lib"))
-              (mkdir (string-append out "/include"))
-              (copy-file "src/withershins.hpp"
-                         (string-append out "/include/withershins.hpp"))
-              (copy-file "src/libwithershins.a"
-                         (string-append out "/lib/libwithershins.a")))
+            (let* ((out (assoc-ref outputs "out"))
+                   (include (string-append out "/include"))
+                   (lib (string-append out "/lib")))
+              (mkdir-p include)
+              (install-file "src/withershins.hpp" include)
+              (mkdir-p lib)
+              (install-file "src/libwithershins.a" lib))
             #t)))))
     (home-page "https://github.com/cameronwhite/withershins";)
     (inputs
diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm
index 9c933a4..1f5b38e 100644
--- a/gnu/packages/conky.scm
+++ b/gnu/packages/conky.scm
@@ -64,7 +64,7 @@
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (mkdir-p bin)
-             (copy-file "src/conky" (string-append bin "/conky"))))
+             (install-file "src/conky" bin)))
          %standard-phases))))
     (inputs
      `(("freetype" ,freetype)
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 6278f66..27193c8 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -68,10 +68,10 @@
               (mkdir-p bin)
               (mkdir-p doc)
               (for-each (lambda (h)
-                          (copy-file h (string-append doc "/" (basename h))))
+                          (install-file h doc))
                         `("License.txt" ,@(find-files "www" ".*\\.html")))
               (for-each (lambda (b)
-                          (copy-file b (string-append bin "/" b)))
+                          (install-file b bin))
                         `("delta" "multidelta" "topformflat")))))
         (alist-delete 'configure %standard-phases))))
     (home-page "http://delta.tigris.org/";)
@@ -212,13 +212,13 @@ tools that process C/C++ code.")
                                       (system* "tar" "xf"
                                                (assoc-ref inputs "afl-src")))
                                (error "tar failed to unpack afl-src"))
-                             (copy-file (string-append patch-dir
-                                                       "/afl-qemu-cpu-inl.h")
-                                        "./afl-qemu-cpu-inl.h")
+                             (install-file (string-append patch-dir
+                                                          
"/afl-qemu-cpu-inl.h")
+                                           ".")
                              (copy-file (string-append afl-dir "/config.h")
                                         "./afl-config.h")
-                             (copy-file (string-append afl-dir "/types.h")
-                                        "./types.h")
+                             (install-file (string-append afl-dir "/types.h")
+                                           ".")
                              (substitute* "afl-qemu-cpu-inl.h"
                                (("\\.\\./\\.\\./config.h") "afl-config.h"))
                              (substitute* (string-append patch-dir
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 3db5527..c6e62ac 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2101,7 +2101,7 @@ to a key in your preferred mode.")
         ;; keep only file of interest
         '(begin
            (for-each delete-file '("dot-emacs.el" "Makefile"))
-           (copy-file "6.945-config/mit-scheme-doc.el" "mit-scheme-doc.el")
+           (install-file "6.945-config/mit-scheme-doc.el" ".")
            (delete-file-recursively "6.945-config")))
        (file-name (string-append name "-" version ".tar.bz2"))
        (method url-fetch)
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 23446ba..dd56af9 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -96,13 +96,13 @@
                                            (assoc-ref inputs "boost")))))
         (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
-           (let ((out (assoc-ref outputs "out")))
-             (mkdir-p (string-append out "/bin"))
-             (mkdir-p (string-append out "/share/librecad"))
-             (copy-file "unix/librecad"
-                        (string-append out "/bin/librecad"))
-             (copy-recursively "unix/resources"
-                               (string-append out "/share/librecad"))))))))
+           (let* ((out   (assoc-ref outputs "out"))
+                  (bin   (string-append out "/bin"))
+                  (share (string-append out "/share/librecad")))
+             (mkdir-p bin)
+             (install-file "unix/librecad" bin)
+             (mkdir-p share)
+             (copy-recursively "unix/resources" share)))))))
     (inputs
      `(("boost" ,boost)
        ("muparser" ,muparser)