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authorpjotrp2017-12-09 13:31:44 +0000
committerpjotrp2017-12-09 13:31:44 +0000
commitbe6c362e51def376af79b05f1d2589b7c57c37aa (patch)
treee9fb914a4a6187d23368d6c918de659ae190aec6 /gn/packages
parent32f78d0be2c3c3c74cdc53be6a780dedd5534e7f (diff)
downloadguix-bioinformatics-be6c362e51def376af79b05f1d2589b7c57c37aa.tar.gz
gemma and ldc
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm4
-rw-r--r--gn/packages/ldc.scm105
2 files changed, 107 insertions, 2 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 871db1d..16630ab 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -86,7 +86,7 @@ numbers.")
(define-public gemma-git-gn2 ; guix candidate
- (let ((commit "dfc7a67aaab9ec752fadd4c29b4fd2646a57c8aa"))
+ (let ((commit "915b65391d4267da75ce3deeba8b9aafb2184c0a"))
(package
(name "gemma-git-gn2")
(version (string-append "0.97-pre5-" (string-take commit 7)))
@@ -98,7 +98,7 @@ numbers.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "12rggrzi8kqm801sbpw0r44lh22xkhh78ys2a49h5xy9spcny4fi"))))
+ "1xvjhhx7djzi2dffqnfwh6w9gn20xqavbwn5yshg0lrr035pabq6"))))
(inputs `(
("gsl" ,gsl)
("eigen" ,eigen)
diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm
index 8caeefe..e2bfd1f 100644
--- a/gn/packages/ldc.scm
+++ b/gn/packages/ldc.scm
@@ -27,9 +27,11 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages gdb)
#:use-module ((gnu packages ldc) #:prefix ldcmain:)
#:use-module (gnu packages libedit)
#:use-module (gnu packages llvm)
+ #:use-module (gnu packages python)
#:use-module (gnu packages textutils)
)
@@ -116,6 +118,109 @@
(base32
"0n7gvalxwfmia4gag53r9qhcnk2cqrw3n4icj1yri0zkgc27pm60"))))))))
+
+(define-public ldc
+ ;; The phobos, druntime and dmd-testsuite dependencies do not have a newer
+ ;; release than 1.1.0-beta4, hence the need to make use of the older-version
+ ;; variable to hold this variable.
+ (let ((older-version "1.6.0"))
+ (package
+ ;; (inherit ldc-bootstrap)
+ (inherit ldcmain:ldc)
+ (name "ldc")
+ (version "1.6.0")
+ ;; Beta version needed to compile various scientific tools that require
+ ;; the newer beta versions, and won't compile successfully with the
+ ;; older stable version.
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/ldc/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0yjiwg8pnlm2286bwdkwasaqw6ys7lymrqvhh5xyb1adha1ndcav"))))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and (unpack "phobos-src" "runtime/phobos")
+ (unpack "druntime-src" "runtime/druntime")
+ (unpack "dmd-testsuite-src" "tests/d2/dmd-testsuite")))))
+ ;; The 'patch-dmd2 step in ldc causes the build to fail since
+ ;; dmd2/root/port.c no longer exists. Arguments needed to have
+ ;; 'patch-dmd2 step removed, but retain everything else.
+ (add-after 'unpack-submodule-sources 'patch-phobos
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "runtime/phobos/std/process.d"
+ (("/bin/sh") (which "sh"))
+ (("echo") (which "echo")))
+ (substitute* "runtime/phobos/std/datetime.d"
+ (("/usr/share/zoneinfo/")
+ (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")))
+ (substitute* "tests/d2/dmd-testsuite/Makefile"
+ (("/bin/bash") (which "bash")))
+ #t)))))
+ (native-inputs
+ `(("llvm" ,llvm)
+ ("clang" ,clang)
+ ;; ("ldc" ,ldc-bootstrap)
+ ("ldc" ,ldcmain:ldc)
+ ("python-lit" ,python-lit)
+ ("python-wrapper" ,python-wrapper)
+ ("unzip" ,unzip)
+ ("gdb" ,gdb)
+ ("phobos-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/phobos/archive/ldc-v"
+ older-version ".tar.gz"))
+ (sha256
+ (base32
+ "0z5v55b9s1ppf0c2ivjq7sbmq688c37c92ihc3qwrbxnqvkkvrlk"))
+ ;; This patch deactivates some tests that depend on network access
+ ;; to pass. It also deactivates some tests that have some reliance
+ ;; on timezone.
+ ;;
+ ;; For the network tests, there's an effort to get a version flag
+ ;; added to deactivate these tests for distribution packagers
+ ;; that is being pursued at
+ ;; <https://forum.dlang.org/post/zmdbdgnzrxyvtpqafvyg@forum.dlang.org>.
+ ;; It also deactivates a test that requires /root
+ (patches (search-patches "ldc-1.1.0-disable-phobos-tests.patch"))))
+ ("druntime-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/druntime/archive/ldc-v"
+ older-version ".tar.gz"))
+ (sha256
+ (base32
+ "07qvrqj6vgakd6qr4x5f70w6zwkzd1li5x8i1b5ywnds1z5lnfp6"))))
+ ("dmd-testsuite-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
+ older-version ".tar.gz"))
+ (sha256
+ (base32
+ "12cak7yqmsgjlflx0dp6fwmwb9dac25amgi86n0bb95ard3547wy"))
+ ;; Remove the gdb tests that fails with a "Error: No such file or
+ ;; directory" error, despite the files being present in the debug
+ ;; files left with the --keep-failed flag to guix build.
+ (patches (search-patches "ldc-1.1.0-disable-dmd-tests.patch")))))))))
+
+(define-public ldc-beta ldc)
+
(define-public ldc-1.1.0-patched ; guix in main line w.o. patch
(let ((version2 "1.1.0")) ; version for libraries
(package