gn: vg: Use G-expressions.

* gn/packages/bioinformatics.scm (vg): Use G-expressions.

1 files changed, 141 insertions, 140 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index e0586fb..3172880 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2353,152 +2353,153 @@ in-memory footprint at the cost of packing and unpacking.")
                (("-mcx16") ""))))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (delete 'configure)    ; no configure script
-         (add-after 'unpack 'patch-source
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; Most of these are so that we can skip bootstrapping some of the sources.
-             (substitute* "Makefile"
-               ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything.
-               (("cairo libzstd")
-                "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate")
-
-               ;; Skip the part where we link static libraries special. It doesn't like the changes we make
-               (("-Wl,-B.*") "\n")
-
-               (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a")
-               ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a")
-                (string-append " " (search-input-file inputs "/lib/libtabixpp.so")))
-               (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc")
-                (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc")))
-
-               (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a")
-               ((" \\$\\(LIB_DIR\\)/libhts\\.a")
-                (string-append " " (search-input-file inputs "/lib/libhts.so")))
-               (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc")
-                (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc")))
-
-               (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a")
-               ((" \\$\\(LIB_DIR\\)/libdeflate\\.a")
-                (string-append " " (search-input-file inputs "/lib/libdeflate.so")))
-
-               ((" \\$\\(LIB_DIR\\)/libvcflib.a")
-                (string-append " " (search-input-file inputs "/lib/libvcflib.so")))
-               ((" \\$\\(BIN_DIR\\)/vcf2tsv")
-                (string-append " " (search-input-file inputs "/bin/vcf2tsv")))
-
-               ((" \\$\\(FASTAHACK_DIR\\)/fastahack")
-                (string-append " " (search-input-file inputs "/bin/fastahack")))
-               (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o")
-                (string-append "+= " (search-input-file inputs "/lib/libfastahack.so")))
-
-               ((" \\$\\(LIB_DIR\\)/libsnappy.a")
-                (string-append " " (search-input-file inputs "/lib/libsnappy.so")))
-
-               ;; Only link against the libraries in the elfutils package.
-               (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf")
-               ((" \\$\\(LIB_DIR\\)/libelf.a")
-                (string-append " " (search-input-file inputs "/lib/libelf.so")))
-               ((" \\$\\(LIB_DIR\\)/libdw.a")
-                (string-append " " (search-input-file inputs "/lib/libdw.so")))
-
-               ((" \\$\\(LIB_DIR\\)/%divsufsort.a")
-                (string-append " " (dirname
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)    ; no configure script
+          (add-after 'unpack 'patch-source
+            (lambda* (#:key inputs #:allow-other-keys)
+              ;; Most of these are so that we can skip bootstrapping some of the sources.
+              (substitute* "Makefile"
+                ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything.
+                (("cairo libzstd")
+                 "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate")
+
+                ;; Skip the part where we link static libraries special. It doesn't like the changes we make
+                (("-Wl,-B.*") "\n")
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a")
+                ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libtabixpp.so")))
+                (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc")
+                 (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc")))
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a")
+                ((" \\$\\(LIB_DIR\\)/libhts\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libhts.so")))
+                (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc")
+                 (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc")))
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a")
+                ((" \\$\\(LIB_DIR\\)/libdeflate\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libdeflate.so")))
+
+                ((" \\$\\(LIB_DIR\\)/libvcflib.a")
+                 (string-append " " (search-input-file inputs "/lib/libvcflib.so")))
+                ((" \\$\\(BIN_DIR\\)/vcf2tsv")
+                 (string-append " " (search-input-file inputs "/bin/vcf2tsv")))
+
+                ((" \\$\\(FASTAHACK_DIR\\)/fastahack")
+                 (string-append " " (search-input-file inputs "/bin/fastahack")))
+                (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o")
+                 (string-append "+= " (search-input-file inputs "/lib/libfastahack.so")))
+
+                ((" \\$\\(LIB_DIR\\)/libsnappy.a")
+                 (string-append " " (search-input-file inputs "/lib/libsnappy.so")))
+
+                ;; Only link against the libraries in the elfutils package.
+                (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf")
+                ((" \\$\\(LIB_DIR\\)/libelf.a")
+                 (string-append " " (search-input-file inputs "/lib/libelf.so")))
+                ((" \\$\\(LIB_DIR\\)/libdw.a")
+                 (string-append " " (search-input-file inputs "/lib/libdw.so")))
+
+                ((" \\$\\(LIB_DIR\\)/%divsufsort.a")
+                 (string-append " " (dirname
                                      (search-input-file inputs "/lib/libdivsufsort.so"))
-                               "%divsufsort.so"))
-               ((" \\$\\(LIB_DIR\\)/libdivsufsort.a")
-                (string-append " " (search-input-file inputs "/lib/libdivsufsort.so")))
-               ((" \\$\\(LIB_DIR\\)/%divsufsort64.a")
-                (string-append " " (dirname
+                                "%divsufsort.so"))
+                ((" \\$\\(LIB_DIR\\)/libdivsufsort.a")
+                 (string-append " " (search-input-file inputs "/lib/libdivsufsort.so")))
+                ((" \\$\\(LIB_DIR\\)/%divsufsort64.a")
+                 (string-append " " (dirname
                                      (search-input-file inputs "/lib/libdivsufsort64.so"))
-                               "%divsufsort64.so"))
-               ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a")
-                (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so")))
-
-               ((" \\$\\(LIB_DIR\\)/libjemalloc.a")
-                (string-append " " (search-input-file inputs "/lib/libjemalloc.a")))
-
-               ((" \\$\\(INC_DIR\\)/sparsehash")
-                (string-append " " (search-input-directory inputs "/include/sparsehash")))
-
-               ((" \\$\\(INC_DIR\\)/raptor2")
-                (string-append " " (search-input-directory inputs "/include/raptor2")))
-               ((" \\$\\(LIB_DIR\\)/libraptor2.a")
-                (string-append " " (search-input-file inputs "/lib/libraptor2.so")))
-               ((" \\$\\(BIN_DIR\\)/rapper")
-                (string-append " " (search-input-file inputs "/bin/rapper"))))))
-         (add-after 'unpack 'link-with-some-shared-libraries
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* '("deps/mmmultimap/CMakeLists.txt"
-                            "deps/xg/CMakeLists.txt"
-                            "deps/xg/deps/mmmulti/CMakeLists.txt")
-               (("\".*libsdsl\\.a\"") "\"-lsdsl\"")
-               (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"")
-               (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"")
-               (("\\$\\{sdsl-lite_INCLUDE\\}")
-                (search-input-directory inputs "/include/sdsl"))
-               (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
-                (dirname
+                                "%divsufsort64.so"))
+                ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a")
+                 (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so")))
+
+                ((" \\$\\(LIB_DIR\\)/libjemalloc.a")
+                 (string-append " " (search-input-file inputs "/lib/libjemalloc.a")))
+
+                ((" \\$\\(INC_DIR\\)/sparsehash")
+                 (string-append " " (search-input-directory inputs "/include/sparsehash")))
+
+                ((" \\$\\(INC_DIR\\)/raptor2")
+                 (string-append " " (search-input-directory inputs "/include/raptor2")))
+                ((" \\$\\(LIB_DIR\\)/libraptor2.a")
+                 (string-append " " (search-input-file inputs "/lib/libraptor2.so")))
+                ((" \\$\\(BIN_DIR\\)/rapper")
+                 (string-append " " (search-input-file inputs "/bin/rapper"))))))
+          (add-after 'unpack 'link-with-some-shared-libraries
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* '("deps/mmmultimap/CMakeLists.txt"
+                             "deps/xg/CMakeLists.txt"
+                             "deps/xg/deps/mmmulti/CMakeLists.txt")
+                (("\".*libsdsl\\.a\"") "\"-lsdsl\"")
+                (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"")
+                (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"")
+                (("\\$\\{sdsl-lite_INCLUDE\\}")
+                 (search-input-directory inputs "/include/sdsl"))
+                (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
+                 (dirname
                   (search-input-file inputs "/include/divsufsort.h"))))))
-         (add-after 'unpack 'dont-build-shared-vgio
-           (lambda _
-             ;; vg will link with libvgio and fail the 'validate-runpath phase.
-             (substitute* "deps/libvgio/CMakeLists.txt"
-               (("TARGETS vgio vgio_static") "TARGETS vgio_static"))))
-         (add-after 'unpack 'fix-fastahack-dependency
-           (lambda _
-             (substitute* (append (list "src/aligner.hpp"
-                                        "src/vg.hpp")
-                                  (find-files "deps/vcflib/src" "\\.cpp$"))
-               (("Fasta.h") "fastahack/Fasta.h"))
-             (substitute* '("deps/vcflib/src/Variant.h"
-                            "src/constructor.hpp"
-                            "src/index_registry.cpp")
-               (("<Fasta.h>") "\"fastahack/Fasta.h\""))))
-         (add-after 'unpack 'adjust-tests
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((bash-tap (assoc-ref inputs "bash-tap")))
-               (substitute* (find-files "test/t")
-                 (("BASH_TAP_ROOT.*")
-                  (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
-                 ((".*bash-tap-bootstrap")
-                  (string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
-               (substitute* "test/t/02_vg_construct.t"
-                 (("../deps/fastahack/fastahack") (which "fastahack"))
-                 (("../bin/vcf2tsv") (which "vcf2tsv")))
-               ;; Lets skip the 9 failing tests for now. They fail with our
-               ;; bash-tap and the bundled one.
-               (substitute* "test/t/02_vg_construct.t"
-                 ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n"))
-               (substitute* "test/t/07_vg_map.t"
-                 ;; Change in fasta's output
-                 (("identity\\) 1 \"") "identity) 1.0 \""))
-               (substitute* '("test/t/07_vg_map.t"
-                              "test/t/33_vg_mpmap.t")
-                 ((".*node id.*") "is $(true) \"\" \"\"\n"))
-               (substitute* "test/t/48_vg_convert.t"
-                 (("true \"vg.*") "true \"true\"\n"))
-               (substitute* "test/t/50_vg_giraffe.t"
-                 ((".*A long read can.*") "is $(true) \"\" \"\"\n")
-                 ((".*A long read has.*") "is $(true) \"\" \"\"\n")
-                 ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n"))
-               ;; Don't test the docs, we're not providing npm
-               (substitute* "Makefile"
-                 ((".*test-docs.*") "")))))
-         (add-after 'build 'build-manpages
-           (lambda* (#:key inputs #:allow-other-keys)
-             (when (assoc-ref inputs "asciidoctor")
-               (invoke "make" "man"))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (install-file "bin/vg" (string-append out "/bin"))
-               (for-each
+          (add-after 'unpack 'dont-build-shared-vgio
+            (lambda _
+              ;; vg will link with libvgio and fail the 'validate-runpath phase.
+              (substitute* "deps/libvgio/CMakeLists.txt"
+                (("TARGETS vgio vgio_static") "TARGETS vgio_static"))))
+          (add-after 'unpack 'fix-fastahack-dependency
+            (lambda _
+              (substitute* (append (list "src/aligner.hpp"
+                                         "src/vg.hpp")
+                                   (find-files "deps/vcflib/src" "\\.cpp$"))
+                (("Fasta.h") "fastahack/Fasta.h"))
+              (substitute* '("deps/vcflib/src/Variant.h"
+                             "src/constructor.hpp"
+                             "src/index_registry.cpp")
+                (("<Fasta.h>") "\"fastahack/Fasta.h\""))))
+          (add-after 'unpack 'adjust-tests
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((bash-tap (assoc-ref inputs "bash-tap")))
+                (substitute* (find-files "test/t")
+                  (("BASH_TAP_ROOT.*")
+                   (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
+                  ((".*bash-tap-bootstrap")
+                   (string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
+                (substitute* "test/t/02_vg_construct.t"
+                  (("../deps/fastahack/fastahack") (which "fastahack"))
+                  (("../bin/vcf2tsv") (which "vcf2tsv")))
+                ;; Lets skip the 9 failing tests for now. They fail with our
+                ;; bash-tap and the bundled one.
+                (substitute* "test/t/02_vg_construct.t"
+                  ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n"))
+                (substitute* "test/t/07_vg_map.t"
+                  ;; Change in fasta's output
+                  (("identity\\) 1 \"") "identity) 1.0 \""))
+                (substitute* '("test/t/07_vg_map.t"
+                               "test/t/33_vg_mpmap.t")
+                  ((".*node id.*") "is $(true) \"\" \"\"\n"))
+                (substitute* "test/t/48_vg_convert.t"
+                  (("true \"vg.*") "true \"true\"\n"))
+                (substitute* "test/t/50_vg_giraffe.t"
+                  ((".*A long read can.*") "is $(true) \"\" \"\"\n")
+                  ((".*A long read has.*") "is $(true) \"\" \"\"\n")
+                  ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n"))
+                ;; Don't test the docs, we're not providing npm
+                (substitute* "Makefile"
+                  ((".*test-docs.*") "")))))
+          (add-after 'build 'build-manpages
+            (lambda* (#:key inputs #:allow-other-keys)
+              (when (assoc-ref inputs "asciidoctor")
+                (invoke "make" "man"))))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (install-file "bin/vg" (string-append out "/bin"))
+                (for-each
                  (lambda (file)
                    (install-file file (string-append out "/share/man/man1")))
                  (find-files "doc/man" "\\.1$"))))))
-       #:test-target "test"))
+      #:test-target "test"))
     (native-inputs
      (append
        (if (supported-package? ruby-asciidoctor)