gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.

* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.

gnu/packages/bioinformatics.scm

@@ -7977,51 +7977,53 @@ other functional sequencing data.")
     (license license:gpl2)))
 
 (define-public r-phantompeakqualtools
-  (package
-    (name "r-phantompeakqualtools")
-    (version "1.2.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/kundajelab/phantompeakqualtools")
-             (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42")))
-       (file-name (string-append name "-" version "-checkout"))
-       (sha256
-        (base32
-         "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f ; There are no tests.
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (delete 'build)
-         (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((script (string-append (assoc-ref outputs "out")
-                                          "/share/scripts")))
-               (install-file "run_spp.R" script)))))))
-    (inputs
-     `(("r" ,r-minimal)))
-    (propagated-inputs
-     `(("r-catools" ,r-catools)
-       ("r-snow" ,r-snow)
-       ("r-snowfall" ,r-snowfall)
-       ("r-bitops" ,r-bitops)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-spp" ,r-spp)
-       ("gawk" ,gawk)
-       ("samtools" ,samtools)
-       ("boost" ,boost)
-       ("gzip" ,gzip)))
-    (home-page "https://github.com/kundajelab/phantompeakqualtools")
-    (synopsis "Informative enrichment for ChIP-seq data")
-    (description "This package computes informative enrichment and quality
+  (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42")
+        (revision "1"))
+    (package
+      (name "r-phantompeakqualtools")
+      (version (git-version "1.2.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/kundajelab/phantompeakqualtools")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; There are no tests.
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'build)
+           (replace 'install
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((script (string-append (assoc-ref outputs "out")
+                                            "/share/scripts")))
+                 (install-file "run_spp.R" script)))))))
+      (inputs
+       `(("r" ,r-minimal)))
+      (propagated-inputs
+       `(("r-catools" ,r-catools)
+         ("r-snow" ,r-snow)
+         ("r-snowfall" ,r-snowfall)
+         ("r-bitops" ,r-bitops)
+         ("r-rsamtools" ,r-rsamtools)
+         ("r-spp" ,r-spp)
+         ("gawk" ,gawk)
+         ("samtools" ,samtools)
+         ("boost" ,boost)
+         ("gzip" ,gzip)))
+      (home-page "https://github.com/kundajelab/phantompeakqualtools")
+      (synopsis "Informative enrichment for ChIP-seq data")
+      (description "This package computes informative enrichment and quality
 measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.  It can also be
 used to obtain robust estimates of the predominant fragment length or
 characteristic tag shift values in these assays.")
-    (license license:bsd-3)))
+      (license license:bsd-3))))
 
 (define-public r-r4rna
   (package