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01/02: gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
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guix-commits |
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Subject: |
01/02: gnu: ncbi-vdb: Ensure that vdb-sqlite is installed. |
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Date: |
Fri, 12 May 2023 15:59:15 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 8ba3bf6564fb95e7bbaf0d32ebb5af7deb5ec365
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri May 12 21:51:41 2023 +0200
gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
The most important change here is the addition of the 'install-libs phase.
All other changes are just the result of switching to G-expressions.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs
phase; use G-expression; drop trailing #T from build phases.
[inputs]: Drop package labels.
---
gnu/packages/bioinformatics.scm | 184 ++++++++++++++++++++--------------------
1 file changed, 92 insertions(+), 92 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 500c418b13..d1a2816466 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7561,99 +7561,99 @@ simultaneously.")
"0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6"))))
(build-system gnu-build-system)
(arguments
- `(#:parallel-build? #f ; not supported
- #:tests? #f ; no "check" target
- #:make-flags '("HAVE_HDF5=1")
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'make-files-writable
- (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
- (add-before 'configure 'set-perl-search-path
- (lambda _
- ;; Work around "dotless @INC" build failure.
- (setenv "PERL5LIB"
- (string-append (getcwd) "/setup:"
- (getenv "PERL5LIB")))
- #t))
- ;; See https://github.com/ncbi/ncbi-vdb/issues/14
- (add-after 'unpack 'patch-krypto-flags
- (lambda _
- (substitute* "libs/krypto/Makefile"
- (("-Wa,-march=generic64\\+aes") "")
- (("-Wa,-march=generic64\\+sse4") ""))
- #t))
- (replace 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- ;; Override include path for libmagic
- (substitute* "setup/package.prl"
- (("name => 'magic', Include => '/usr/include'")
- (string-append "name=> 'magic', Include => '"
- (assoc-ref inputs "libmagic")
- "/include" "'")))
-
- ;; Install kdf5 library (needed by sra-tools)
- (substitute* "build/Makefile.install"
- (("LIBRARIES_TO_INSTALL =")
- "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX)
kdf5.$(VERSION_SHLX)"))
-
- (substitute* "build/Makefile.env"
- (("CFLAGS =" prefix)
- (string-append prefix "-msse2 ")))
-
- ;; Override search path for ngs-java
- (substitute* "setup/package.prl"
- (("/usr/local/ngs/ngs-java")
- (assoc-ref inputs "java-ngs")))
-
- ;; The 'configure' script doesn't recognize things like
- ;; '--enable-fast-install'.
- (invoke "./configure"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" (assoc-ref outputs "out"))
- (string-append "--debug")
- (string-append "--with-xml2-prefix="
- (assoc-ref inputs "libxml2"))
- (string-append "--with-ngs-sdk-prefix="
- (assoc-ref inputs "ngs-sdk"))
- (string-append "--with-hdf5-prefix="
- (assoc-ref inputs "hdf5")))
- #t)))
- (add-after 'install 'install-interfaces
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Install interface libraries. On i686 the interface libraries
- ;; are installed to "linux/gcc/i386", so we need to use the Linux
- ;; architecture name ("i386") instead of the target system prefix
- ;; ("i686").
- (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
- (copy-recursively (string-append
- "build/ncbi-vdb/linux/gcc/"
- ,(platform-linux-architecture
- (lookup-platform-by-target-or-system
- (or (%current-target-system)
- (%current-system))))
- "/rel/ilib")
- (string-append (assoc-ref outputs "out")
- "/ilib"))
- ;; Install interface headers
- (copy-recursively "interfaces"
- (string-append (assoc-ref outputs "out")
- "/include"))
- #t))
- ;; These files are needed by sra-tools.
- (add-after 'install 'install-configuration-files
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
- (mkdir target)
- (install-file "libs/kfg/default.kfg" target)
- (install-file "libs/kfg/certs.kfg" target))
- #t)))))
+ (list
+ #:parallel-build? #f ; not supported
+ #:tests? #f ; no "check" target
+ #:make-flags '(list "HAVE_HDF5=1")
+ #:phases
+ #~(modify-phases %standard-phases
+ #;
+ (add-after 'unpack 'make-files-writable
+ (lambda _ (for-each make-file-writable (find-files "." ".*"))))
+ (add-before 'configure 'set-perl-search-path
+ (lambda _
+ ;; Work around "dotless @INC" build failure.
+ (setenv "PERL5LIB"
+ (string-append (getcwd) "/setup:"
+ (getenv "PERL5LIB")))))
+ ;; See https://github.com/ncbi/ncbi-vdb/issues/14
+ (add-after 'unpack 'patch-krypto-flags
+ (lambda _
+ (substitute* "libs/krypto/Makefile"
+ (("-Wa,-march=generic64\\+aes") "")
+ (("-Wa,-march=generic64\\+sse4") ""))))
+ (replace 'configure
+ (lambda _
+ ;; Override include path for libmagic
+ (substitute* "setup/package.prl"
+ (("name => 'magic', Include => '/usr/include'")
+ (string-append "name=> 'magic', Include => '"
+ #$(this-package-input "file")
+ "/include" "'")))
+
+ ;; Install kdf5 library (needed by sra-tools)
+ (substitute* "build/Makefile.install"
+ (("LIBRARIES_TO_INSTALL =")
+ "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX)
kdf5.$(VERSION_SHLX)"))
+
+ (substitute* "build/Makefile.env"
+ (("CFLAGS =" prefix)
+ (string-append prefix "-msse2 ")))
+
+ ;; Override search path for ngs-java
+ (substitute* "setup/package.prl"
+ (("/usr/local/ngs/ngs-java")
+ #$(this-package-input "java-ngs")))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (invoke "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" #$output)
+ (string-append "--debug")
+ (string-append "--with-xml2-prefix="
+ #$(this-package-input "libxml2"))
+ (string-append "--with-ngs-sdk-prefix="
+ #$(this-package-input "ngs-sdk"))
+ (string-append "--with-hdf5-prefix="
+ #$(this-package-input "hdf5")))))
+ (add-after 'install 'install-interfaces
+ (lambda _
+ ;; Install interface libraries. On i686 the interface libraries
+ ;; are installed to "linux/gcc/i386", so we need to use the Linux
+ ;; architecture name ("i386") instead of the target system prefix
+ ;; ("i686").
+ (mkdir (string-append #$output "/ilib"))
+ (copy-recursively (string-append
+ "build/ncbi-vdb/linux/gcc/"
+ #$(platform-linux-architecture
+ (lookup-platform-by-target-or-system
+ (or (%current-target-system)
+ (%current-system))))
+ "/rel/ilib")
+ (string-append #$output "/ilib"))
+ ;; Install interface headers
+ (copy-recursively "interfaces"
+ (string-append #$output "/include"))))
+ (add-after 'install-interfaces 'install-libs
+ (lambda _
+ (copy-recursively (string-append
+ "build/ncbi-vdb/linux/gcc/"
+ #$(platform-linux-architecture
+ (lookup-platform-by-target-or-system
+ (or (%current-target-system)
+ (%current-system))))
+ "/rel/lib")
+ (string-append #$output "/lib"))))
+ ;; These files are needed by sra-tools.
+ (add-after 'install 'install-configuration-files
+ (lambda _
+ (let ((target (string-append #$output "/kfg")))
+ (mkdir target)
+ (install-file "libs/kfg/default.kfg" target)
+ (install-file "libs/kfg/certs.kfg" target)))))))
(inputs
- `(("libxml2" ,libxml2)
- ("ngs-sdk" ,ngs-sdk)
- ("java-ngs" ,java-ngs)
- ("libmagic" ,file)
- ("hdf5" ,hdf5)))
+ (list file hdf5 java-ngs libxml2 ngs-sdk ))
(native-inputs (list perl))
;; NCBI-VDB requires SSE capability.
(supported-systems '("i686-linux" "x86_64-linux"))