gnu: dropseq-tools: Improve style.

* gnu/packages/bioinformatics.scm (dropseq-tools): Run guix style.
[arguments]: Use G-expressions.
<#:phases>: Improve style of phases 'record-references and 'install,
'install-links.
[inputs]: Drop input labels.
[description]: Run guix style.

Change-Id: Icf50199a850e3f339395279cdd077c950a027065
Signed-off-by: Andreas Enge <andreas@enge.fr>

1 files changed, 110 insertions, 110 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1911dd82063..82f768cdef1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17577,130 +17577,130 @@ contains
        (uri "http://mccarrolllab.com/download/1276/")
        (file-name (string-append "dropseq-tools-" version ".zip"))
        (sha256
-        (base32
-         "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
+        (base32 "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
        ;; Delete bundled libraries
        (modules '((guix build utils)))
        (snippet
         '(begin
-           (for-each delete-file (find-files "jar/lib" "\\.jar$"))
+           (for-each delete-file
+                     (find-files "jar/lib" "\\.jar$"))
            (delete-file-recursively "3rdParty")))))
     (build-system ant-build-system)
     (arguments
-     `(#:tests? #f                      ; test data are not included
-       #:test-target "test"
-       #:build-target "all"
-       #:source-dir "public/src/"
-       #:jdk ,icedtea-8
-       #:make-flags
-       (list ,#~(string-append "-Dpicard.executable.dir="
-                               #$(this-package-input "java-picard")
-                               "/share/java/"))
-       #:modules ((ice-9 match)
+     (list
+      #:tests? #f ;test data are not included
+      #:test-target "test"
+      #:build-target "all"
+      #:source-dir "public/src/"
+      #:jdk icedtea-8
+      #:make-flags
+      #~(list (string-append "-Dpicard.executable.dir="
+                             #$(this-package-input "java-picard")
+                             "/share/java/"))
+      #:modules `((ice-9 match)
                   (srfi srfi-1)
                   (guix build utils)
                   (guix build java-utils)
                   (guix build ant-build-system))
-       #:phases
-       (modify-phases %standard-phases
-         ;; FIXME: fails with "java.io.FileNotFoundException:
-         ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar"
-         (delete 'generate-jar-indices)
-         ;; All dependencies must be linked to "lib", because that's where
-         ;; they will be searched for when the Class-Path property of the
-         ;; manifest is computed.
-         (add-after 'unpack 'record-references
-           (lambda* (#:key inputs #:allow-other-keys)
-             (mkdir-p "jar/lib")
-             (let ((dirs (filter-map (match-lambda
-                                       ((name . dir)
-                                        (if (and (string-prefix? "java-" name)
-                                                 (not (string=? name "java-testng")))
-                                            dir #f)))
-                                     inputs)))
-               (for-each (lambda (jar)
-                           (symlink jar (string-append "jar/lib/" (basename jar))))
-                         (append-map (lambda (dir) (find-files dir "\\.jar$"))
-                                     dirs)))))
-         ;; There is no installation target
-         (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out     (assoc-ref outputs "out"))
-                    (bin     (string-append out "/bin"))
-                    (share   (string-append out "/share/java/"))
-                    (lib     (string-append share "/lib/"))
-                    (scripts (list "BAMTagHistogram"
-                                   "BAMTagofTagCounts"
-                                   "BaseDistributionAtReadPosition"
-                                   "CollapseBarcodesInPlace"
-                                   "CollapseTagWithContext"
-                                   "ConvertToRefFlat"
-                                   "CreateIntervalsFiles"
-                                   "DetectBeadSynthesisErrors"
-                                   "DigitalExpression"
-                                   "Drop-seq_alignment.sh"
-                                   "FilterBAM"
-                                   "FilterBAMByTag"
-                                   "GatherGeneGCLength"
-                                   "GatherMolecularBarcodeDistributionByGene"
-                                   "GatherReadQualityMetrics"
-                                   "PolyATrimmer"
-                                   "ReduceGTF"
-                                   "SelectCellsByNumTranscripts"
-                                   "SingleCellRnaSeqMetricsCollector"
-                                   "TagBamWithReadSequenceExtended"
-                                   "TagReadWithGeneExon"
-                                   "TagReadWithInterval"
-                                   "TrimStartingSequence"
-                                   "ValidateReference")))
-               (for-each mkdir-p (list bin share lib))
-               (install-file "dist/dropseq.jar" share)
-               (for-each (lambda (script)
-                           (chmod script #o555)
-                           (install-file script bin))
-                         scripts)
-               (substitute* (map (lambda (script)
-                                   (string-append bin "/" script))
-                                 scripts)
-                 (("^java") (which "java"))
-                 (("jar_deploy_dir=.*")
-                  (string-append "jar_deploy_dir=" share "\n"))))))
-         ;; FIXME: We do this after stripping jars because we don't want it to
-         ;; copy all these jars and strip them.  We only want to install
-         ;; links.  Arguably, this is a problem with the ant-build-system.
-         (add-after 'strip-jar-timestamps 'install-links
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out     (assoc-ref outputs "out"))
-                    (share   (string-append out "/share/java/"))
-                    (lib     (string-append share "/lib/")))
-               (for-each (lambda (jar)
-                           (symlink (readlink jar)
-                                    (string-append lib (basename jar))))
-                         (find-files "jar/lib" "\\.jar$"))))))))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; FIXME: fails with "java.io.FileNotFoundException:
+          ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar"
+          (delete 'generate-jar-indices)
+          ;; All dependencies must be linked to "lib", because that's where
+          ;; they will be searched for when the Class-Path property of the
+          ;; manifest is computed.
+          (add-after 'unpack 'record-references
+            (lambda* (#:key inputs #:allow-other-keys)
+              (mkdir-p "jar/lib")
+              (let ((dirs (filter-map
+                           (match-lambda
+                             ((name . dir)
+                              (and (string-prefix? "java-" name)
+                                   (not (string=? name "java-testng"))
+                                   dir)))
+                           inputs)))
+                (for-each
+                 (lambda (jar)
+                   (symlink jar (string-append "jar/lib/" (basename jar))))
+                 (append-map (lambda (dir)
+                               (find-files dir "\\.jar$"))
+                             dirs)))))
+          ;; There is no installation target
+          (replace 'install
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((bin (string-append #$output "/bin"))
+                     (share (string-append #$output "/share/java/"))
+                     (scripts (list "BAMTagHistogram"
+                                    "BAMTagofTagCounts"
+                                    "BaseDistributionAtReadPosition"
+                                    "CollapseBarcodesInPlace"
+                                    "CollapseTagWithContext"
+                                    "ConvertToRefFlat"
+                                    "CreateIntervalsFiles"
+                                    "DetectBeadSynthesisErrors"
+                                    "DigitalExpression"
+                                    "Drop-seq_alignment.sh"
+                                    "FilterBAM"
+                                    "FilterBAMByTag"
+                                    "GatherGeneGCLength"
+                                    "GatherMolecularBarcodeDistributionByGene"
+                                    "GatherReadQualityMetrics"
+                                    "PolyATrimmer"
+                                    "ReduceGTF"
+                                    "SelectCellsByNumTranscripts"
+                                    "SingleCellRnaSeqMetricsCollector"
+                                    "TagBamWithReadSequenceExtended"
+                                    "TagReadWithGeneExon"
+                                    "TagReadWithInterval"
+                                    "TrimStartingSequence"
+                                    "ValidateReference")))
+                (install-file "dist/dropseq.jar" share)
+                (for-each (lambda (script)
+                            (chmod script #o555)
+                            (install-file script bin))
+                          scripts)
+                (with-directory-excursion bin
+                  (substitute* scripts
+                    (("^java")
+                     (which "java"))
+                    (("jar_deploy_dir=.*")
+                     (string-append "jar_deploy_dir=" share "\n")))))))
+          ;; FIXME: We do this after stripping jars because we don't want it to
+          ;; copy all these jars and strip them.  We only want to install
+          ;; links.  Arguably, this is a problem with the ant-build-system.
+          (add-after 'strip-jar-timestamps 'install-links
+            (lambda _
+              (let ((lib (string-append #$output "/share/java/lib/")))
+                (mkdir-p lib)
+                (for-each (lambda (jar)
+                            (symlink (readlink jar)
+                                     (string-append lib (basename jar))))
+                          (find-files "jar/lib" "\\.jar$"))))))))
     (inputs
-     `(("jdk" ,icedtea-8)
-       ("java-picard" ,java-picard-2.10.3)
-       ("java-log4j-1.2-api" ,java-log4j-1.2-api)
-       ("java-commons-math3" ,java-commons-math3)
-       ("java-commons-jexl2" ,java-commons-jexl-2)
-       ("java-commons-collections4" ,java-commons-collections4)
-       ("java-commons-lang2" ,java-commons-lang)
-       ("java-commons-io" ,java-commons-io)
-       ("java-snappy-1.0.3-rc3" ,java-snappy-1)
-       ("java-guava" ,java-guava)
-       ("java-la4j" ,java-la4j)
-       ("java-biojava-core" ,java-biojava-core-4.0)
-       ("java-biojava-alignment" ,java-biojava-alignment-4.0)
-       ("java-jdistlib" ,java-jdistlib)
-       ("java-simple-xml" ,java-simple-xml)
-       ("java-snakeyaml" ,java-snakeyaml)))
-    (native-inputs
-     (list unzip java-testng))
+     (list icedtea-8
+           java-picard-2.10.3
+           java-log4j-1.2-api
+           java-commons-math3
+           java-commons-jexl-2
+           java-commons-collections4
+           java-commons-lang
+           java-commons-io
+           java-snappy-1
+           java-guava
+           java-la4j
+           java-biojava-core-4.0
+           java-biojava-alignment-4.0
+           java-jdistlib
+           java-simple-xml
+           java-snakeyaml))
+    (native-inputs (list unzip java-testng))
     (home-page "http://mccarrolllab.com/dropseq/")
     (synopsis "Tools for Drop-seq analyses")
-    (description "Drop-seq is a technology to enable biologists to
-analyze RNA expression genome-wide in thousands of individual cells at
-once.  This package provides tools to perform Drop-seq analyses.")
+    (description
+     "Drop-seq is a technology to enable biologists to analyze RNA expression
+genome-wide in thousands of individual cells at once.  This package provides
+tools to perform Drop-seq analyses.")
     (license license:expat)))
 
 (define-public pigx-rnaseq