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-rw-r--r--gn/packages/bioinformatics.scm92
-rw-r--r--gn/packages/genenetwork.scm36
-rw-r--r--gn/packages/ldc.scm326
-rw-r--r--gn/packages/llvm.scm65
-rw-r--r--gn/packages/pocl.scm328
-rw-r--r--gn/packages/python.scm2
-rw-r--r--gn/packages/statistics.scm28
7 files changed, 206 insertions, 671 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index f62949d..e16c28e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -37,7 +37,7 @@
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
- #:use-module (gnu packages ldc)
+ #:use-module (gn packages ldc)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
@@ -772,41 +772,6 @@ to sample traits. Also includes a number of utility functions for
data manipulation and visualization.")
(license license:gpl2+))))
-(define-public qtlreaper
- (package
- (name "qtlreaper")
- (version "1.1.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"
- ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb"))
- ))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))
- (build-system python-build-system)
- ;; (native-inputs
- ;; `(("python-setuptools" ,python-setuptools)))
- (arguments
- `(#:python ,python-2
- #:tests? #f)) ; no 'setup.py test'
- (home-page "http://qtlreaper.sourceforge.net/")
- (synopsis "Tool for scanning expression data for QTLs")
- (description
- "It is essentially the batch-oriented version of WebQTL. It
-requires, as input, expression data from members of a set of
-recombinant inbred lines and genotype information for the same
-lines. It searches for an association between each expression trait
-and all genotypes and evaluates that association by a permutation
-test. For the permutation test, it performs only as many permutations
-as are necessary to define the empirical P-value to a reasonable
-precision. It also performs bootstrap resampling to estimate the
-confidence region for the location of a putative QTL.")
- (license license:gpl2+)))
-
(define-public plink2
(package
(name "plink2")
@@ -956,44 +921,38 @@ association studies (GWAS).")
(license license:gpl3))))
(define-public sambamba
- (let ((commit "c810c7ef14957f16288c205fd7b9d25c4ae7005d"))
- ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+ (let ((commit "5a33d571339c966477c1f70ed08f64051f7b41c1"))
(package
(name "sambamba")
- (version (string-append "0.5.9-1." (string-take commit 7)))
+ (version (string-append "0.6.5-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/roelj/sambamba.git")
- ;;(url "https://github.com/pjotrp/sambamba.git")
+ (url "https://github.com/pjotrp/sambamba.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0c4c13f021sl7mf5xc2v8dbwsz775n8dlsrrn7qa6qgbx05n54dv"))))
- ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
+ "05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5"))))
(build-system gnu-build-system)
+ (outputs '("out"
+ "debug")) ;retain debug symbols - note that -O2 is used
(native-inputs
`(("ldc" ,ldc)
- ;;("lz4" ,lz4)
- ("rdmd" ,rdmd)
+ ("lz4" ,lz4)
+ ("coreutils" ,coreutils) ; for env
("zlib" ,zlib)
("perl" ,perl) ; Needed for htslib
("ruby" ,ruby) ; Needed for htslib
- ("python" ,python) ; Needed for htslib
+ ("python" ,python-2) ; Needed for htslib
("gcc" ,gcc)
- ("lz4-src"
- ,(origin
- (method url-fetch)
- (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz")
- (sha256
- (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20"))))
+ ("which" ,which)
("htslib-src"
,(origin
(method url-fetch)
(uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz")
;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
- ;;(file-name "htslib-1.3.tar.gz")
+ (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz")
(sha256
(base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
@@ -1003,13 +962,12 @@ association studies (GWAS).")
(method git-fetch)
(uri (git-reference
(url "https://github.com/biod/BioD.git")
- (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
- (file-name "biod-src")
+ (commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")))
+ (file-name (string-append "biod-src-" (string-take commit 7) ".tar.gz"))
(sha256
- (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
+ (base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))
(arguments
- `(#:tests? #f
- #:make-flags (list "-f" "Makefile.guix")
+ `(#:tests? #f ; no tests available
#:phases
(modify-phases %standard-phases
(delete 'configure)
@@ -1022,16 +980,13 @@ association studies (GWAS).")
(and (with-directory-excursion "htslib"
(zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
"--strip-components=1")))
- (with-directory-excursion "lz4"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
- "--strip-components=1")))
(zero? (system* "rm" "-r" "BioD"))
(zero? (system* "ln" "--symbolic" "--no-target-directory"
(assoc-ref inputs "biod-src") "BioD")))))
(replace
'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "sambamba-ldmd2-64" "CC=gcc" "D_COMPILER=ldc2"
+ (zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2"
(string-append "LDC_LIB_PATH="
(assoc-ref inputs "ldc")
"/lib")))))
@@ -1041,16 +996,15 @@ association studies (GWAS).")
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "build/sambamba" bin)))))))
(home-page "https://github.com/lomereiter/sambamba")
- (synopsis "A tool for working with SAM and BAM files written in D.")
+ (synopsis "Fast tool for working with SAM, BAM and CRAM files written in D.")
(description
- "Sambamba is a high performance modern robust and fast tool (and
-library), written in the D programming language, for working with SAM
-and BAM files. Current parallelised functionality is an important
-subset of samtools functionality, including view, index, sort,
-markdup, and depth.")
+ "Sambamba is a high performance modern robust and fast
+tool (and library), written in the D programming language, for working
+with SAM, BAM and CRAM files. Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
(license license:gpl2+))))
-
(define-public vcflib
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
(package
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index a7317c6..dfbba02 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -87,6 +87,41 @@
(description #f)
(license #f)))
+(define-public qtlreaper
+ (let ((commit "71fbbe2b35e4f54937be2d54d09fb71d25fe5fad"))
+ (package
+ (name "qtlreaper")
+ (version (string-append "1.1-gn2" (string-take commit 7) ))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; (url "https://github.com/genenetwork/genenetwork2.git")
+ (url "https://github.com/pjotrp/QTLreaper.git")
+ (commit commit)))
+ (file-name (string-append name "-" (string-take commit 7)))
+ (sha256
+ (base32
+ "0g0v20lh7773cm2xdqz6xzwjw4130y265n79z5x20p5aja5y5kmg"))))
+ (build-system python-build-system)
+ ;; (native-inputs
+ ;; `(("python-setuptools" ,python-setuptools)))
+ (arguments
+ `(#:python ,python-2
+ ))
+ (home-page "http://qtlreaper.sourceforge.net/")
+ (synopsis "Tool for scanning expression data for QTLs")
+ (description
+ "Batch-oriented version of WebQTL. It requires, as input,
+expression data from members of a set of recombinant inbred lines and
+genotype information for the same lines. It searches for an
+association between each expression trait and all genotypes and
+evaluates that association by a permutation test. For the permutation
+test, it performs only as many permutations as are necessary to define
+the empirical P-value to a reasonable precision. It also performs
+bootstrap resampling to estimate the confidence region for the
+location of a putative QTL.")
+ (license license:gpl2+))))
+
(define-public genenetwork1
(let ((commit "d622c803b"))
(package
@@ -157,6 +192,7 @@
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
+ ("r-ctl" ,r-ctl)
("r-wgcna" ,r-wgcna)
("r-qtl" ,r-qtl)
("redis" ,redis)
diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm
index 45ba1b4..7fa91b9 100644
--- a/gn/packages/ldc.scm
+++ b/gn/packages/ldc.scm
@@ -17,7 +17,7 @@
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
-(define-module (gnu packages ldc)
+(define-module (gn packages ldc)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
@@ -27,152 +27,15 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
+ #:use-module ((gnu packages ldc) #:prefix ldcmain:)
#:use-module (gnu packages libedit)
#:use-module (gnu packages llvm)
#:use-module (gnu packages textutils)
#:use-module (gnu packages zip))
-(define-public rdmd
- (let ((commit "da0a2e0a379b08294015eec9d531f1e5dd4226f0"))
- (package
- (name "rdmd")
- (version (string-append "v2.070.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/D-Programming-Language/tools.git")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
- (build-system gnu-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (delete 'check) ; There is no Makefile, so there's no 'make check'.
- (replace
- 'build
- (lambda _
- (zero? (system* "ldc2" "rdmd.d"))))
- (replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "rdmd" bin)))))))
- (native-inputs
- `(("ldc" ,ldc)))
- (home-page "https://github.com/D-Programming-Language/tools/")
- (synopsis "Specialized equivalent to 'make' for the D language")
- (description
- "rdmd is a companion to the dmd compiler that simplifies the typical
-edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
-make and other tools, rdmd uses the relative dates of the files involved to
-minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
-and freshness without requiring additional information from the user.")
- (license license:boost1.0))))
-
-(define-public ldc-0.16.1
- (package
- (name "ldc")
- (version "0.16.1")
- (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
- "1jvilxx0rpqmkbja4m69fhd5g09697xq7vyqp2hz4hvxmmmv4j40"))))
- (build-system cmake-build-system)
- ;; LDC currently only supports the x86_64 and i686 architectures.
- (supported-systems '("x86_64-linux" "i686-linux"))
- (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")))))
- (add-after 'unpack-submodule-sources 'patch-dmd2
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "dmd2/root/port.c"
- ((" ::isnan") " isnan")
- ((" ::isinf") " isinf")
- (("#undef isnan") "")
- (("#undef isinf") ""))
- #t))
- (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)))))
- (inputs
- `(("libconfig" ,libconfig)
- ("libedit" ,libedit)
- ("tzdata" ,tzdata)
- ("zlib" ,zlib)))
- (native-inputs
- `(("llvm" ,llvm-3.7)
- ("clang" ,clang-3.7)
- ("unzip" ,unzip)
- ("phobos-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/phobos/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "0sgdj0536c4nb118yiw1f8lqy5d3g3lpg9l99l165lk9xy45l9z4"))
- (patches (search-patches "ldc-disable-tests.patch"))))
- ("druntime-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/druntime/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "0z4mkyddx6c4sy1vqgqvavz55083dsxws681qkh93jh1rpby9yg6"))))
- ("dmd-testsuite-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "0yc6miidzgl9k33ygk7xcppmfd6kivqj02cvv4fmkbs3qz4yy3z1"))))))
- (home-page "http://wiki.dlang.org/LDC")
- (synopsis "LLVM compiler for the D programming language")
- (description
- "LDC is a compiler for the D programming language. It is based on the
-latest DMD frontend and uses LLVM as backend.")
- ;; Most of the code is released under BSD-3, except for code originally
- ;; written for GDC, which is released under GPLv2+, and the DMD frontend,
- ;; which is released under the "Boost Software License version 1.0".
- (license (list license:bsd-3
- license:gpl2+
- license:boost1.0))))
-
(define-public ldc-0.17.2
(package
- (inherit ldc)
+ (inherit ldcmain:ldc)
(name "ldc")
(version "0.17.2")
(source (origin
@@ -220,6 +83,7 @@ latest DMD frontend and uses LLVM as backend.")
(native-inputs
`(("llvm" ,llvm-3.7)
("clang" ,clang-3.7)
+ ("zlib" ,zlib)
("unzip" ,unzip)
("phobos-src"
,(origin
@@ -227,6 +91,7 @@ latest DMD frontend and uses LLVM as backend.")
(uri (string-append
"https://github.com/ldc-developers/phobos/archive/ldc-v"
version ".tar.gz"))
+ (file-name (string-append "ldc-phobos-" version ".tar.gz"))
(sha256
(base32
"07hh3ic3r755mq9hn9gfr0wlc5y8cr91xz2ydb6gqy4zy8jgp5s9"))))
@@ -236,6 +101,7 @@ latest DMD frontend and uses LLVM as backend.")
(uri (string-append
"https://github.com/ldc-developers/druntime/archive/ldc-v"
version ".tar.gz"))
+ (file-name (string-append "ldc-druntime-" version ".tar.gz"))
(sha256
(base32
"1m1dhday9dl3s04njmd29z7ism2xn2ksb9qlrwzykdgz27b3dk6x"))))
@@ -245,78 +111,124 @@ latest DMD frontend and uses LLVM as backend.")
(uri (string-append
"https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
version ".tar.gz"))
+ (file-name (string-append "testsuite-" version ".tar.gz"))
(sha256
(base32
"0n7gvalxwfmia4gag53r9qhcnk2cqrw3n4icj1yri0zkgc27pm60"))))))))
-(define-public ldc-1.1.0-beta4
- (package
- (inherit ldc)
- (name "ldc")
- (version "1.1.0-beta4")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/ldc/archive/v"
+(define-public ldc-1.1.0-beta6
+ (let ((version2 "1.1.0-beta4")) ; libraries have not been updated
+ (package
+ (inherit ldcmain:ldc)
+ (name "ldc")
+ (version "1.1.0-beta6")
+ (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
+ "0n53brlkm86jjkppy9xmzx7nyxykzj68kcxgv8q7d10s5hfscxs8"))))
+ (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")))))
+ (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)))
+ #:tests? #f))
+ (native-inputs
+ `(("llvm" ,llvm-3.7)
+ ("ldc" ,ldc-0.17.2)
+ ("zlib" ,zlib)
+ ("phobos-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/phobos/archive/ldc-v"
+ version2 ".tar.gz")) ; older version
+ (file-name (string-append "ldc-phobos-" version2 ".tar.gz"))
+ (sha256
+ (base32
+ "1iwy5rs0rqkicj1zfsa5yqvk8ard99bfr8g69qmhlbzb98q0kpks"))))
+ ("druntime-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/druntime/archive/ldc-v"
+ version2 ".tar.gz"))
+ (file-name (string-append "ldc-druntime-" version2 ".tar.gz"))
+ (sha256
+ (base32
+ "1qsiw5lz1pr8ms9myjf8b94nqi7f1781k226jvxwnhkjg11d0s63"))))
+ ("dmd-testsuite-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
+ version2 ".tar.gz")) ; version is behind
+ (file-name (string-append "dmd-testsuite-" version2 ".tar.gz"))
+ (sha256
+ (base32
+ "0jp54hyi75i9g41rvgmm3zg21yzv57q8dghrhb432rb0n9j15mbp")))))))))
+
+(define-public ldc ldc-1.1.0-beta6)
+
+(define-public rdmd
+ (package
+ (name "rdmd")
+ (version "v2.072.1") ;; remove v when putting in mainline
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/dlang/tools/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04n6sbz6l658s32f7zilpbi9m8a1m4g5wrgl44igkvla30niy5yn"))))
- (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")))))
- (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)))
- #:tests? #f))
- (native-inputs
- `(("llvm" ,llvm-3.7)
- ("ldc" ,ldc-0.17.2)
- ("phobos-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/phobos/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "1iwy5rs0rqkicj1zfsa5yqvk8ard99bfr8g69qmhlbzb98q0kpks"))))
- ("druntime-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/druntime/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "1qsiw5lz1pr8ms9myjf8b94nqi7f1781k226jvxwnhkjg11d0s63"))))
- ("dmd-testsuite-src"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v"
- version ".tar.gz"))
- (sha256
- (base32
- "0jp54hyi75i9g41rvgmm3zg21yzv57q8dghrhb432rb0n9j15mbp"))))))))
-
-(define-public ldc ldc-1.1.0-beta4)
+ "0ryn4fv1mj8c8d7y4lrr43baahl3z7sk5bryj9kd829paz573va6"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check) ; There is no Makefile, so there's no 'make check'.
+ (replace
+ 'build
+ (lambda _
+ (zero? (system* "ldc2" "rdmd.d"))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "rdmd" bin)))))))
+ (native-inputs
+ `(("ldc" ,ldc)))
+ (home-page "https://github.com/D-Programming-Language/tools/")
+ (synopsis "Specialized equivalent to 'make' for the D language")
+ (description
+ "rdmd is a companion to the dmd compiler that simplifies the typical
+edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
+make and other tools, rdmd uses the relative dates of the files involved to
+minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
+and freshness without requiring additional information from the user.")
+ (license license:boost1.0)))
diff --git a/gn/packages/llvm.scm b/gn/packages/llvm.scm
deleted file mode 100644
index 607f7c2..0000000
--- a/gn/packages/llvm.scm
+++ /dev/null
@@ -1,65 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gn packages llvm)
- #:use-module (guix packages)
- #:use-module (guix licenses)
- #:use-module (guix download)
- #:use-module (guix utils)
- #:use-module (guix build-system gnu)
- #:use-module (guix build-system cmake)
- #:use-module (gnu packages)
- #:use-module (gnu packages gcc)
- #:use-module (gnu packages bootstrap) ;glibc-dynamic-linker
- #:use-module (gnu packages perl)
- #:use-module (gnu packages python)
- #:use-module (gnu packages xml))
-
-
-(define-public llvm
-(package
- (name "llvm")
- (version "3.7.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://llvm.org/releases/"
- version "/llvm-" version ".src.tar.xz"))
- (sha256
- (base32
- "1masakdp9g2dan1yrazg7md5am2vacbkb3nahb3dchpc1knr8xxy"))))
- (build-system cmake-build-system)
- (native-inputs
- `(("python" ,python-wrapper)
- ("perl" ,perl)))
- (arguments
- `(#:configure-flags '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
- "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE")))
- (home-page "http://www.llvm.org")
- (synopsis "Optimizing compiler infrastructure")
- (description
- "LLVM is a compiler infrastructure designed for compile-time, link-time,
-runtime, and idle-time optimization of programs from arbitrary programming
-languages. It currently supports compilation of C and C++ programs, using
-front-ends derived from GCC 4.0.1. A new front-end for the C family of
-languages is in development. The compiler infrastructure includes mirror sets
-of programming tools as well as libraries with equivalent functionality.")
- (license ncsa)))
diff --git a/gn/packages/pocl.scm b/gn/packages/pocl.scm
deleted file mode 100644
index 7d61526..0000000
--- a/gn/packages/pocl.scm
+++ /dev/null
@@ -1,328 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gn packages pocl)
- #:use-module ((guix licenses) #:prefix license:)
- #:use-module (guix git-download)
- #:use-module (guix download)
- #:use-module (guix utils)
- #:use-module (guix build-system gnu)
- #:use-module (guix build-system cmake)
- #:use-module (guix packages)
- #:use-module (gnu packages)
- #:use-module (srfi srfi-1)
- #:use-module (gnu packages algebra)
- #:use-module (gnu packages autotools)
- #:use-module (gnu packages curl)
- #:use-module (gnu packages boost)
- #:use-module (gnu packages bootstrap)
- #:use-module (gnu packages base)
- #:use-module (gnu packages gawk)
- #:use-module (gnu packages cmake)
- #:use-module (gnu packages gcc)
- #:use-module (gnu packages glib)
- #:use-module (gnu packages image)
- #:use-module (gnu packages video)
- #:use-module (gnu packages textutils)
- #:use-module (gnu packages gl)
- #:use-module (gnu packages llvm)
- #:use-module (gnu packages pkg-config)
- #:use-module (gnu packages maths)
- #:use-module (gnu packages mpi)
- #:use-module (gnu packages web)
- #:use-module (gnu packages perl)
- #:use-module (gnu packages python)
- #:use-module (gnu packages xorg)
- #:use-module (gnu packages xml)
- #:use-module (gnu packages version-control)
- #:use-module (gnu packages ruby)
- #:use-module (gnu packages gnupg)
- #:use-module ((gnu packages zip) #:prefix gnuzip:)
- #:use-module (gnu packages linux))
-
-(define-public pocl
-(let ((commit "7aefc52"))
- (package
- (name "pocl")
- (version (string-append "v09rc-" commit ))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pocl/pocl.git")
- (commit commit)))
- (file-name (string-append name "-" commit))
- (sha256
- (base32
- "03wbcxkx1w5kx0crangsnah0xq218bhb99vglmn00wcjhhw80qim"))))
-(native-inputs `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)
- ("cmake" ,cmake)
- ("pkg-config" ,pkg-config)))
-(inputs `(("python" ,python-2)
- ("boost" ,boost)
- ("dbus" ,dbus)
- ("clang" ,clang-3.7.1)
- ("clang-runtime" ,clang-runtime-3.7.1)
- ("enca" ,enca)
- ("eudev" ,eudev)
- ("fftw-openmpi" ,fftw-openmpi)
- ("glew" ,glew)
- ("hwloc" ,hwloc)
- ("libcap" ,libcap)
- ("libjpeg" ,libjpeg)
- ("libltdl" ,libltdl)
- ("libtiff" ,libtiff)
- ("llvm" ,llvm-3.7.1)
- ("ocl-icd" ,ocl-icd)
- ("opencl-headers" ,opencl-headers)
- ("mesa-utils" ,mesa-utils)
- ("openmpi" ,openmpi)
- ("perl" ,perl)
- ("randrproto" ,randrproto)
- ("libxrandr" ,libxrandr)
- ("xineramaproto" ,xineramaproto)
- ("libxinerama" ,libxinerama)
- ("libxcursor" ,libxcursor)
- ("fftw-openmpi" ,fftw-openmpi)))
- (build-system gnu-build-system)
- (arguments
- `(#:configure-flags '("--enable-icd")
- #:tests? #f
- #:phases
- (modify-phases %standard-phases
- (add-before
- 'configure 'rewrite-usr-bin
- (lambda _
- (zero? (system* "./autogen.sh")))))))
- (synopsis "pocl: Portable Computing Language (pocl) aims to become a MIT-licensed
- open source implementation of the OpenCL standard which can be easily adapted for
- new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
- (description "Portable Computing Language (pocl) aims to become a MIT-licensed
- open source implementation of the OpenCL standard which can be easily adapted for
- new targets and devices, both for homogeneous CPU and heterogenous GPUs/accelerators.")
- (home-page "http://portablecl.org/")
- (license license:gpl2))))
-
-(define-public ocl-icd
- (package
- (name "ocl-icd")
- (version "2.2.9")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc"))))
- (inputs `(("zip" ,gnuzip:zip)
- ("autoconf" ,autoconf)
- ("automake" ,automake)
- ("ruby" ,ruby)
- ("libtool" ,libtool)
- ("opencl-headers" ,opencl-headers)
- ("libgcrypt" ,libgcrypt)))
- (build-system gnu-build-system)
- (arguments
- '(#:phases (modify-phases %standard-phases
- (add-after 'unpack `bootstrap
- (lambda _
- (zero? (system* "autoreconf" "-vfi")))))))
- (home-page "https://forge.imag.fr/projects/ocl-icd/")
- (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).")
- (description "OpenCL implementations are provided as ICD (Installable Client Driver).
- An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project.
- This free ICD Loader can load any (free or non free) ICD")
- (license license:gpl2)))
-
- (define-public opencl-headers
-(let ((commit "c1770dc"))
- (package
- (name "opencl-headers")
- (version (string-append "2.1-" commit ))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/KhronosGroup/OpenCL-Headers.git")
- (commit commit)))
- (file-name (string-append name "-" commit))
- (sha256
- (base32
- "0m9fkblqja0686i2jjqiszvq3df95gp01a2674xknlmkd6525rck"))))
- (propagated-inputs '())
- (inputs '())
- (native-inputs '())
- (build-system gnu-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (delete 'build)
- (delete 'check)
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (copy-recursively "." (string-append
- (assoc-ref outputs "out")
- "/include/CL")))))))
- (synopsis "The Khronos OpenCL headers")
- (description "This package provides the Khronos OpenCL headers")
- (home-page "https://www.khronos.org/registry/cl/")
- (license license:gpl2))))
-
-(define (clang-runtime-from-llvm llvm hash)
- (package
- (name "clang-runtime")
- (version (package-version llvm-3.7.1))
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://llvm.org/releases/"
- version "/compiler-rt-" version ".src.tar.xz"))
- (sha256
- (base32
- "10c1mz2q4bdq9bqfgr3dirc6hz1h3sq8573srd5q5lr7m7j6jiwx"))))
- (build-system cmake-build-system)
- (native-inputs (package-native-inputs llvm))
- (inputs
- `(("llvm" ,llvm)))
- (arguments
- `(;; Don't use '-g' during the build to save space.
- #:build-type "Release"))
-
- (home-page "http://compiler-rt.llvm.org")
- (synopsis "Runtime library for Clang/LLVM")
- (description
- "The \"clang-runtime\" library provides the implementations of run-time
-functions for C and C++ programs. It also provides header files that allow C
-and C++ source code to interface with the \"sanitization\" passes of the clang
-compiler. In LLVM this library is called \"compiler-rt\".")
- (license license:ncsa)
-
- ;; <http://compiler-rt.llvm.org/> doesn't list MIPS as supported.
- (supported-systems (delete "mips64el-linux" %supported-systems))))
-
-(define (clang-from-llvm llvm clang-runtime hash)
- (package
- (name "clang")
- (version (package-version llvm-3.7.1))
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://llvm.org/releases/"
- version "/cfe-" version ".src.tar.xz"))
- (sha256
- (base32
- "0x065d0w9b51xvdjxwfzjxng0gzpbx45fgiaxpap45ragi61dqjn"))
- (patches (list (search-patch "clang-libc-search-path.patch")))))
- ;; Using cmake allows us to treat llvm as an external library. There
- ;; doesn't seem to be any way to do this with clang's autotools-based
- ;; build system.
- (build-system cmake-build-system)
- (native-inputs (package-native-inputs llvm))
- (inputs
- `(("libxml2" ,libxml2)
- ("libstdc++-4.9", libstdc++-4.9)
- ("python" ,python-2)
- ("gcc-lib" ,gcc "lib")
- ,@(package-inputs llvm)))
- (propagated-inputs
- `(("llvm" ,llvm)
- ("clang-runtime" ,clang-runtime)))
- (arguments
- `(#:configure-flags
- (list "-DCLANG_INCLUDE_TESTS=True"
-
- ;; Find libgcc_s, crtbegin.o, and crtend.o.
- (string-append "-DGCC_INSTALL_PREFIX="
- (assoc-ref %build-inputs "gcc-lib"))
-
- ;; Use a sane default include directory.
- (string-append "-DC_INCLUDE_DIRS="
- (assoc-ref %build-inputs "libc")
- "/include"))
-
- ;; Don't use '-g' during the build to save space.
- #:build-type "Release"
-
- #:phases (modify-phases %standard-phases
- (add-after
- 'unpack 'set-glibc-file-names
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((libc (assoc-ref inputs "libc"))
- (compiler-rt (assoc-ref inputs "clang-runtime")))
- (substitute* "lib/Driver/Tools.cpp"
- ;; Patch the 'getLinuxDynamicLinker' function to that
- ;; it uses the right dynamic linker file name.
- (("/lib64/ld-linux-x86-64.so.2")
- (string-append libc
- ,(glibc-dynamic-linker)))
-
- ;; Link to libclang_rt files from clang-runtime.
- (("TC\\.getDriver\\(\\)\\.ResourceDir")
- (string-append "\"" compiler-rt "\"")))
-
- ;; Same for libc's libdir, to allow crt1.o & co. to be
- ;; found.
- (substitute* "lib/Driver/ToolChains.cpp"
- (("@GLIBC_LIBDIR@")
- (string-append libc "/lib")))))))))
-
- ;; Clang supports the same environment variables as GCC.
- (native-search-paths
- (list (search-path-specification
- (variable "CPATH")
- (files '("include")))
- (search-path-specification
- (variable "LIBRARY_PATH")
- (files '("lib" "lib64")))))
-
- (home-page "http://clang.llvm.org")
- (synopsis "C language family frontend for LLVM")
- (description
- "Clang is a compiler front end for the C, C++, Objective-C and
-Objective-C++ programming languages. It uses LLVM as its back end. The Clang
-project includes the Clang front end, the Clang static analyzer, and several
-code analysis tools.")
- (license license:ncsa)))
-
-(define-public llvm-3.7.1
- (package (inherit llvm)
- (version "3.7.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://llvm.org/releases/"
- version "/llvm-" version ".src.tar.xz"))
- (sha256
- (base32
- "1masakdp9g2dan1yrazg7md5am2vacbkb3nahb3dchpc1knr8xxy"))))))
-
-(define-public clang-runtime-3.7.1
- (clang-runtime-from-llvm
- llvm-3.7.1
- "0dl1kbrhz96djsxqr61iw5h788s7ncfpfb7aayixky1bhdaydcx4"))
-
-(define-public clang-3.7.1
- (clang-from-llvm llvm clang-runtime
- "12yv3jwdjcbkrx7zjm8wh4jrvb59v8fdw4mnmz3zc1jb00p9k07w"))
-
-
-
-
-
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index e4196cf..7dbd968 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -396,7 +396,7 @@ version ".tgz"))
(native-inputs
`(("python2-setuptools" ,python2-setuptools)))
(propagated-inputs
- `(("python2-pillow" ,python2-pillow)))
+ `(("python2-pil" ,python2-pil)))
(arguments
`(
#:python ,python-2
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index dbe6b99..b83ccf2 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -14,6 +14,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
@@ -333,7 +334,7 @@
(uri (git-reference
(url "https://github.com/genenetwork/pylmm.git")
(commit commit)))
- (file-name (string-append name "-" commit))
+ (file-name (string-append name "-" commit))
(sha256
(base32
"0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
@@ -362,3 +363,28 @@
(description "Fast and lightweight linear mixed-model (LMM) solver
for use in genome-wide association studies (GWAS).")
(license license:agpl3+))))
+
+(define-public r-ctl
+ (package
+ (name "r-ctl")
+ (version "1.0.0-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/ctl_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "12hrrql9wz43s1d3sfyzlqzx7ajrl3hvf96776ik6icbm8by8h6j"))))
+ (build-system r-build-system)
+ (inputs `(
+ ("r-qtl" ,r-qtl)
+ ))
+ (home-page "https://github.com/DannyArends/CTLmapping")
+ (synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL)")
+ (description "Analysis of experimental crosses to identify genetic
+markers associated with correlation changes in quantitative
+traits (CTL). The additional correlation information obtained can be
+combined with QTL information to perform de novo reconstruction of
+interaction networks.")
+ (license license:gpl3)))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 02:01:52 +0000