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d14'>diff)parent63abd1e2a36d48e1f8f7057a4c844b9cf5733be7 (diff)downloadguix-c166a88dea354f0fb253e7d389e68f1b11fe1de4.tar.gz
guix-c166a88dea354f0fb253e7d389e68f1b11fe1de4.zip
Merge branch 'master' into core-updates
Diffstat
-rw-r--r--gnu/build/install.scm2
-rw-r--r--gnu/local.mk4
-rw-r--r--gnu/packages/bioconductor.scm26
-rw-r--r--gnu/packages/bioinformatics.scm658
-rw-r--r--gnu/packages/build-tools.scm58
-rw-r--r--gnu/packages/crypto.scm4
-rw-r--r--gnu/packages/dns.scm4
-rw-r--r--gnu/packages/education.scm8
-rw-r--r--gnu/packages/emacs.scm49
-rw-r--r--gnu/packages/gnome.scm6
-rw-r--r--gnu/packages/linux.scm46
-rw-r--r--gnu/packages/lxqt.scm72
-rw-r--r--gnu/packages/mpd.scm4
-rw-r--r--gnu/packages/patches/crossmap-allow-system-pysam.patch121
-rw-r--r--gnu/packages/patches/delly-use-system-libraries.patch56
-rw-r--r--gnu/packages/patches/liblxqt-include.patch14
-rw-r--r--gnu/packages/patches/tophat-build-with-later-seqan.patch24
-rw-r--r--gnu/packages/python-crypto.scm12
-rw-r--r--gnu/packages/python.scm54
-rw-r--r--gnu/packages/samba.scm4
-rw-r--r--gnu/packages/ssh.scm4
-rw-r--r--gnu/packages/tex.scm189
-rw-r--r--gnu/packages/video.scm4
-rw-r--r--gnu/packages/xorg.scm8
24 files changed, 797 insertions, 634 deletions
diff --git a/gnu/build/install.scm b/gnu/build/install.scm
index 5a5e703872..c602d69489 100644
--- a/gnu/build/install.scm
+++ b/gnu/build/install.scm
@@ -199,7 +199,7 @@ This is used to create the self-contained tarballs with 'guix pack'."
(mkdir-p* %root-profile)
(symlink* profile
(string-append %root-profile "/guix-profile-1-link"))
- (symlink* (string-append %root-profile "/guix-profile-1-link")
+ (symlink* "guix-profile-1-link"
(string-append %root-profile "/guix-profile"))
(mkdir-p* "/root")
diff --git a/gnu/local.mk b/gnu/local.mk
index befe3c4b33..e0bd43164c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -635,7 +635,6 @@ dist_patch_DATA = \
%D%/packages/patches/cracklib-fix-buffer-overflow.patch \
%D%/packages/patches/crawl-upgrade-saves.patch \
%D%/packages/patches/crda-optional-gcrypt.patch \
- %D%/packages/patches/crossmap-allow-system-pysam.patch \
%D%/packages/patches/clucene-contribs-lib.patch \
%D%/packages/patches/cube-nocheck.patch \
%D%/packages/patches/cursynth-wave-rand.patch \
@@ -644,7 +643,6 @@ dist_patch_DATA = \
%D%/packages/patches/datamash-arm-tests.patch \
%D%/packages/patches/dbus-helper-search-path.patch \
%D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
- %D%/packages/patches/delly-use-system-libraries.patch \
%D%/packages/patches/dfu-programmer-fix-libusb.patch \
%D%/packages/patches/diffutils-gets-undeclared.patch \
%D%/packages/patches/diffutils-getopt.patch \
@@ -890,7 +888,6 @@ dist_patch_DATA = \
%D%/packages/patches/libjxr-fix-function-signature.patch \
%D%/packages/patches/libjxr-fix-typos.patch \
%D%/packages/patches/libotr-test-auth-fix.patch \
- %D%/packages/patches/liblxqt-include.patch \
%D%/packages/patches/libmad-armv7-thumb-pt1.patch \
%D%/packages/patches/libmad-armv7-thumb-pt2.patch \
%D%/packages/patches/libmad-frame-length.patch \
@@ -1180,7 +1177,6 @@ dist_patch_DATA = \
%D%/packages/patches/tk-find-library.patch \
%D%/packages/patches/ttf2eot-cstddef.patch \
%D%/packages/patches/ttfautohint-source-date-epoch.patch \
- %D%/packages/patches/tophat-build-with-later-seqan.patch \
%D%/packages/patches/totem-meson-easy-codec.patch \
%D%/packages/patches/tuxpaint-stamps-path.patch \
%D%/packages/patches/twinkle-include-qregexpvalidator.patch \
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b779855b2..92b67453f6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -913,3 +913,29 @@ can be analyzed regarding their minimal, maximal and average distances between
barcodes. Finally, reads that start with a (possibly mutated) barcode can be
demultiplexed, i.e. assigned to their original reference barcode.")
(license license:gpl2)))
+
+(define-public r-ruvseq
+ (package
+ (name "r-ruvseq")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RUVSeq" version))
+ (sha256
+ (base32
+ "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
+ (properties `((upstream-name . "RUVSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-edaseq" ,r-edaseq)
+ ("r-edger" ,r-edger)
+ ("r-mass" ,r-mass)))
+ (home-page "https://github.com/drisso/RUVSeq")
+ (synopsis "Remove unwanted variation from RNA-Seq data")
+ (description
+ "This package implements methods to @dfn{remove unwanted variation} (RUV)
+of Risso et al. (2014) for the normalization of RNA-Seq read counts between
+samples.")
+ (license license:artistic2.0)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1e04081ceb..96ea07bdc4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1332,7 +1332,7 @@ gapped, local, and paired-end alignment modes.")
(define-public tophat
(package
(name "tophat")
- (version "2.1.0")
+ (version "2.1.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1340,13 +1340,12 @@ gapped, local, and paired-end alignment modes.")
version ".tar.gz"))
(sha256
(base32
- "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
- (patches (search-patches "tophat-build-with-later-seqan.patch"))
+ "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled SeqAn and samtools
- (delete-file-recursively "src/SeqAn-1.3")
+ (delete-file-recursively "src/SeqAn-1.4.2")
(delete-file-recursively "src/samtools-0.1.18")
#t))))
(build-system gnu-build-system)
@@ -1383,7 +1382,7 @@ gapped, local, and paired-end alignment modes.")
("python" ,python-2)
("perl" ,perl)
("zlib" ,zlib)
- ("seqan" ,seqan)))
+ ("seqan" ,seqan-1)))
(home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
(synopsis "Spliced read mapper for RNA-Seq data")
(description
@@ -1450,13 +1449,14 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
(name "bwa-pssm")
(version "0.5.11")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
- "archive/" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pkerpedjiev/bwa-pssm.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
+ "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r"))))
(build-system gnu-build-system)
(inputs
`(("gdsl" ,gdsl)
@@ -1474,40 +1474,38 @@ the original BWA alignment program and shares the genome index structure as
well as many of the command line options.")
(license license:gpl3+)))
-(define-public python2-bx-python
+(define-public python-bx-python
(package
- (name "python2-bx-python")
- (version "0.7.3")
+ (name "python-bx-python")
+ (version "0.8.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "bx-python" version))
(sha256
(base32
- "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (substitute* "setup.py"
- ;; remove dependency on outdated "distribute" module
- (("^from distribute_setup import use_setuptools") "")
- (("^use_setuptools\\(\\)") ""))
- #t))))
+ "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
(build-system python-build-system)
- (arguments
- `(#:tests? #f ;tests fail because test data are not included
- #:python ,python-2))
+ ;; Tests fail because test data are not included
+ (arguments '(#:tests? #f))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-six" ,python-six)))
(inputs
- `(("python-numpy" ,python2-numpy)
- ("zlib" ,zlib)))
+ `(("zlib" ,zlib)))
(native-inputs
- `(("python-nose" ,python2-nose)))
- (home-page "http://bitbucket.org/james_taylor/bx-python/")
+ `(("python-lzo" ,python-lzo)
+ ("python-nose" ,python-nose)
+ ("python-cython" ,python-cython)))
+ (home-page "https://github.com/bxlab/bx-python")
(synopsis "Tools for manipulating biological data")
(description
"bx-python provides tools for manipulating biological data, particularly
multiple sequence alignments.")
(license license:expat)))
+(define-public python2-bx-python
+ (package-with-python2 python-bx-python))
+
(define-public python-pysam
(package
(name "python-pysam")
@@ -1597,19 +1595,19 @@ also includes an interface for tabix.")
(define-public python-twobitreader
(package
(name "python-twobitreader")
- (version "3.1.4")
+ (version "3.1.6")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "twobitreader" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/benjschiller/twobitreader")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
+ "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62"))))
(build-system python-build-system)
- (arguments
- '(;; Tests are not distributed in the PyPi release.
- ;; TODO Try building from the Git repo or asking the upstream maintainer
- ;; to distribute the tests on PyPi.
- #:tests? #f))
+ ;; Tests are not included
+ (arguments '(#:tests? #f))
(native-inputs
`(("python-sphinx" ,python-sphinx)))
(home-page "https://github.com/benjschiller/twobitreader")
@@ -1896,31 +1894,18 @@ time.")
(define-public crossmap
(package
(name "crossmap")
- (version "0.2.1")
+ (version "0.2.9")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
- version ".tar.gz"))
+ (uri (pypi-uri "CrossMap" version))
(sha256
(base32
- "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
- ;; This patch has been sent upstream already and is available
- ;; for download from Sourceforge, but it has not been merged.
- (patches (search-patches "crossmap-allow-system-pysam.patch"))
- (modules '((guix build utils)))
- (snippet '(begin
- ;; remove bundled copy of pysam
- (delete-file-recursively "lib/pysam")
- #t))))
+ "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
(build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'set-env
- (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
+ (arguments `(#:python ,python-2))
(inputs
- `(("python-numpy" ,python2-numpy)
+ `(("python-bx-python" ,python2-bx-python)
+ ("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("zlib" ,zlib)))
(native-inputs
@@ -1934,22 +1919,46 @@ files between different genome assemblies. It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(license license:gpl2+)))
+(define-public python-dnaio
+ (package
+ (name "python-dnaio")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "dnaio" version))
+ (sha256
+ (base32
+ "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-pytest" ,python-pytest)
+ ("python-xopen" ,python-xopen)))
+ (home-page "https://github.com/marcelm/dnaio/")
+ (synopsis "Read FASTA and FASTQ files efficiently")
+ (description
+ "dnaio is a Python library for fast parsing of FASTQ and also FASTA
+files. The code was previously part of the cutadapt tool.")
+ (license license:expat)))
+
(define-public cutadapt
(package
(name "cutadapt")
- (version "1.16")
+ (version "1.18")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/marcelm/cutadapt.git")
(commit (string-append "v" version))))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
+ "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg"))))
(build-system python-build-system)
(inputs
- `(("python-xopen" ,python-xopen)))
+ `(("python-dnaio" ,python-dnaio)
+ ("python-xopen" ,python-xopen)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)))
@@ -2044,15 +2053,15 @@ accessing bigWig files.")
(version "4.4.0")
(source
(origin
- (method url-fetch)
+ (method git-fetch)
;; Source from GitHub so that tests are included.
- (uri
- (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (git-reference
+ (url "https://github.com/jeetsukumaran/DendroPy.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn"))))
+ "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9"))))
(build-system python-build-system)
(home-page "http://packages.python.org/DendroPy/")
(synopsis "Library for phylogenetics and phylogenetic computing")
@@ -2082,14 +2091,14 @@ trees (phylogenies) and characters.")
(define-public python-py2bit
(package
(name "python-py2bit")
- (version "0.2.1")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py2bit" version))
(sha256
(base32
- "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
+ "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
(build-system python-build-system)
(home-page "https://github.com/dpryan79/py2bit")
(synopsis "Access 2bit files using lib2bit")
@@ -2101,7 +2110,7 @@ with Python.")
(define-public deeptools
(package
(name "deeptools")
- (version "3.1.2")
+ (version "3.1.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2110,7 +2119,7 @@ with Python.")
(file-name (git-file-name name version))
(sha256
(base32
- "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd"))))
+ "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -2146,42 +2155,42 @@ identify enrichments with functional annotations of the genome.")
(define-public delly
(package
(name "delly")
- (version "0.7.7")
+ (version "0.7.9")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/tobiasrausch/delly/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dellytools/delly.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
- (patches (search-patches "delly-use-system-libraries.patch"))))
+ (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/htslib")
+ #t))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests to run.
- #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+ #:make-flags
+ (list "PARALLEL=1" ; Allow parallel execution at run-time.
+ (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda _
- (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
- (templates (string-append (assoc-ref %outputs "out")
+ (add-after 'install 'install-templates
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((templates (string-append (assoc-ref outputs "out")
"/share/delly/templates")))
- (mkdir-p bin)
(mkdir-p templates)
(copy-recursively "excludeTemplates" templates)
- (install-file "src/cov" bin)
- (install-file "src/delly" bin)
- (install-file "src/dpe" bin)))))))
- (native-inputs
- `(("python" ,python-2)))
+ #t))))))
(inputs
`(("boost" ,boost)
("htslib" ,htslib)
("zlib" ,zlib)
("bzip2" ,bzip2)))
- (home-page "https://github.com/tobiasrausch/delly")
+ (home-page "https://github.com/dellytools/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
that can discover and genotype deletions, tandem duplications, inversions and
@@ -2195,14 +2204,14 @@ accurately delineate genomic rearrangements throughout the genome.")
(name "diamond")
(version "0.9.22")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/bbuchfink/diamond/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/bbuchfink/diamond.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
+ "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -2230,13 +2239,14 @@ data and settings.")
(version "1.6.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/maaskola/discrover/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/maaskola/discrover.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
+ "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -2264,106 +2274,102 @@ of nucleic acid binding proteins.")
(license license:gpl3+)))
(define-public eigensoft
- (let ((revision "1")
- (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
- (package
- (name "eigensoft")
- (version (string-append "6.1.2-"
- revision "."
- (string-take commit 9)))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/DReichLab/EIG.git")
- (commit commit)))
- (file-name (string-append "eigensoft-" commit "-checkout"))
- (sha256
- (base32
- "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
- (modules '((guix build utils)))
- ;; Remove pre-built binaries.
- (snippet '(begin
- (delete-file-recursively "bin")
- (mkdir "bin")
- #t))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; There are no tests.
- #:make-flags '("CC=gcc")
- #:phases
- (modify-phases %standard-phases
- ;; There is no configure phase, but the Makefile is in a
- ;; sub-directory.
- (replace 'configure
- (lambda _
- (chdir "src")
- ;; The link flags are incomplete.
- (substitute* "Makefile"
- (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
- #t))
- ;; The provided install target only copies executables to
- ;; the "bin" directory in the build root.
- (add-after 'install 'actually-install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "../bin" ".*"))
- #t))))))
- (inputs
- `(("gsl" ,gsl)
- ("lapack" ,lapack)
- ("openblas" ,openblas)
- ("perl" ,perl)
- ("gfortran" ,gfortran "lib")))
- (home-page "https://github.com/DReichLab/EIG")
- (synopsis "Tools for population genetics")
- (description "The EIGENSOFT package provides tools for population
+ (package
+ (name "eigensoft")
+ (version "7.2.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DReichLab/EIG.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k"))
+ (modules '((guix build utils)))
+ ;; Remove pre-built binaries.
+ (snippet '(begin
+ (delete-file-recursively "bin")
+ (mkdir "bin")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ #:make-flags '("CC=gcc")
+ #:phases
+ (modify-phases %standard-phases
+ ;; There is no configure phase, but the Makefile is in a
+ ;; sub-directory.
+ (replace 'configure
+ (lambda _ (chdir "src") #t))
+ ;; The provided install target only copies executables to
+ ;; the "bin" directory in the build root.
+ (add-after 'install 'actually-install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "../bin" ".*"))
+ #t))))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("lapack" ,lapack)
+ ("openblas" ,openblas)
+ ("perl" ,perl)
+ ("gfortran" ,gfortran "lib")))
+ (home-page "https://github.com/DReichLab/EIG")
+ (synopsis "Tools for population genetics")
+ (description "The EIGENSOFT package provides tools for population
genetics and stratification correction. EIGENSOFT implements methods commonly
used in population genetics analyses such as PCA, computation of Tracy-Widom
statistics, and finding related individuals in structured populations. It
comes with a built-in plotting script and supports multiple file formats and
quantitative phenotypes.")
- ;; The license of the eigensoft tools is Expat, but since it's
- ;; linking with the GNU Scientific Library (GSL) the effective
- ;; license is the GPL.
- (license license:gpl3+))))
+ ;; The license of the eigensoft tools is Expat, but since it's
+ ;; linking with the GNU Scientific Library (GSL) the effective
+ ;; license is the GPL.
+ (license license:gpl3+)))
(define-public edirect
(package
(name "edirect")
- (version "4.10")
+ (version "10.2.20181018")
(source (origin
(method url-fetch)
- (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
- "versions/2016-05-03/edirect.tar.gz"))
+ (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
+ "/versions/" version
+ "/edirect-" version ".tar.gz"))
(sha256
(base32
- "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
+ "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7"))))
(build-system perl-build-system)
(arguments
- `(#:tests? #f ;no "check" target
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
+ (delete 'check) ; simple check after install
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((target (string-append (assoc-ref outputs "out")
- "/bin")))
- (mkdir-p target)
- (install-file "edirect.pl" target)
- #t)))
- (add-after
- 'install 'wrap-program
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
- (let* ((out (assoc-ref outputs "out"))
- (path (getenv "PERL5LIB")))
- (wrap-program (string-append out "/bin/edirect.pl")
- `("PERL5LIB" ":" prefix (,path)))))))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "edirect.pl"
+ (string-append (assoc-ref outputs "out") "/bin"))
+ #t))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PERL5LIB")))
+ (wrap-program (string-append out "/bin/edirect.pl")
+ `("PERL5LIB" ":" prefix (,path))))
+ #t))
+ (add-after 'wrap-program 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke (string-append (assoc-ref outputs "out")
+ "/bin/edirect.pl")
+ "-filter" "-help")
+ #t)))))
(inputs
`(("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
@@ -2379,6 +2385,7 @@ quantitative phenotypes.")
("perl-net-http" ,perl-net-http)
("perl-uri" ,perl-uri)
("perl-www-robotrules" ,perl-www-robotrules)
+ ("perl-xml-simple" ,perl-xml-simple)
("perl" ,perl)))
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
@@ -2474,17 +2481,16 @@ ChIP-Seq, and analysis of metagenomic data.")
(define-public express-beta-diversity
(package
(name "express-beta-diversity")
- (version "1.0.7")
+ (version "1.0.8")
(source (origin
- (method url-fetch)
- (uri
- (string-append
- "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dparks1134/ExpressBetaDiversity.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
+ "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -2492,17 +2498,13 @@ ChIP-Seq, and analysis of metagenomic data.")
(delete 'configure)
(add-before 'build 'enter-source (lambda _ (chdir "source") #t))
(replace 'check
- (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
- "-u"))))
- (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
+ (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t))
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out")
- "/bin")))
- (mkdir-p bin)
- (install-file "scripts/convertToEBD.py" bin)
- (install-file "bin/ExpressBetaDiversity" bin)
- #t))))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "../scripts/convertToEBD.py" bin)
+ (install-file "../bin/ExpressBetaDiversity" bin)
+ #t))))))
(inputs
`(("python" ,python-2)))
(home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
@@ -2535,31 +2537,30 @@ similarity of community members.")
(delete 'configure)
(replace 'build
(lambda* (#:key source #:allow-other-keys)
- (and (zero? (system* "gcc"
- "-O3"
- "-finline-functions"
- "-funroll-loops"
- "-Wall"
- "-o"
- "FastTree"
- source
- "-lm"))
- (zero? (system* "gcc"
- "-DOPENMP"
- "-fopenmp"
- "-O3"
- "-finline-functions"
- "-funroll-loops"
- "-Wall"
- "-o"
- "FastTreeMP"
- source
- "-lm")))))
+ (invoke "gcc"
+ "-O3"
+ "-finline-functions"
+ "-funroll-loops"
+ "-Wall"
+ "-o"
+ "FastTree"
+ source
+ "-lm")
+ (invoke "gcc"
+ "-DOPENMP"
+ "-fopenmp"
+ "-O3"
+ "-finline-functions"
+ "-funroll-loops"
+ "-Wall"
+ "-o"
+ "FastTreeMP"
+ source
+ "-lm")
+ #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out")
- "/bin")))
- (mkdir-p bin)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "FastTree" bin)
(install-file "FastTreeMP" bin)
#t))))))
@@ -2606,38 +2607,39 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(define-public flexbar
(package
(name "flexbar")
- (version "2.5")
+ (version "3.4.0")
(source (origin
- (method url-fetch)
- (uri
- (string-append "mirror://sourceforge/flexbar/"
- version "/flexbar_v" version "_src.tgz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/seqan/flexbar.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
+ "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2"))))
(build-system cmake-build-system)
(arguments
- `(#:configure-flags (list
- (string-append "-DFLEXBAR_BINARY_DIR="
- (assoc-ref %outputs "out")
- "/bin/"))
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key outputs #:allow-other-keys)
- (setenv "PATH" (string-append
- (assoc-ref outputs "out") "/bin:"
- (getenv "PATH")))
- (chdir "../flexbar_v2.5_src/test")
- (zero? (system* "bash" "flexbar_validate.sh"))))
- (delete 'install))))
+ (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
+ (with-directory-excursion "../source/test"
+ (invoke "bash" "flexbar_test.sh"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out")))
+ (bin (string-append out "/bin/")))
+ (install-file "flexbar" bin))
+ #t)))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("seqan" ,seqan)))
- (home-page "http://flexbar.sourceforge.net")
+ (home-page "https://github.com/seqan/flexbar")
(synopsis "Barcode and adapter removal tool for sequencing platforms")
(description
"Flexbar preprocesses high-throughput nucleotide sequencing data
@@ -2646,7 +2648,7 @@ Moreover, trimming and filtering features are provided. Flexbar increases
read mapping rates and improves genome and transcriptome assemblies. It
supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
- (license license:gpl3)))
+ (license license:bsd-3)))
(define-public fraggenescan
(package
@@ -3741,75 +3743,48 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(define-public khmer
(package
(name "khmer")
- (version "2.0")
+ (version "2.1.2")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "khmer" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dib-lab/khmer.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
- (patches (search-patches "khmer-use-libraries.patch"))))
+ "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m"))
+ (patches (search-patches "khmer-use-libraries.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled libraries. We do not replace the bundled seqan
+ ;; as it is a modified subset of the old version 1.4.1.
+ ;;
+ ;; We do not replace the bundled MurmurHash as the canonical
+ ;; repository for this code 'SMHasher' is unsuitable for providing
+ ;; a library. See
+ ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
+ (delete-file-recursively "third-party/zlib")
+ (delete-file-recursively "third-party/bzip2")
+ #t))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'set-paths
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Delete bundled libraries.
- (delete-file-recursively "third-party/zlib")
- (delete-file-recursively "third-party/bzip2")
- ;; Replace bundled seqan.
- (let* ((seqan-all "third-party/seqan")
- (seqan-include (string-append
- seqan-all "/core/include")))
- (delete-file-recursively seqan-all)
- (copy-recursively (string-append (assoc-ref inputs "seqan")
- "/include/seqan")
- (string-append seqan-include "/seqan")))
- ;; We do not replace the bundled MurmurHash as the canonical
- ;; repository for this code 'SMHasher' is unsuitable for
- ;; providing a library. See
- ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
- #t))
(add-after 'unpack 'set-cc
- (lambda _
- (setenv "CC" "gcc")
- #t))
- ;; It is simpler to test after installation.
- (delete 'check)
- (add-after 'install 'post-install-check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (setenv "PATH"
- (string-append
- (getenv "PATH")
- ":"
- (assoc-ref outputs "out")
- "/bin"))
- (setenv "PYTHONPATH"
- (string-append
- (getenv "PYTHONPATH")
- ":"
- out
- "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3)
- "/site-packages"))
- (with-directory-excursion "build"
- (zero? (system* "nosetests" "khmer" "--attr"
- "!known_failing")))))))))
+ (lambda _ (setenv "CC" "gcc") #t))
+ ;; FIXME: This fails with "permission denied".
+ (delete 'reset-gzip-timestamps))))
(native-inputs
- `(("seqan" ,seqan)
- ("python-nose" ,python-nose)))
+ `(("python-cython" ,python-cython)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
(inputs
`(("zlib" ,zlib)
("bzip2" ,bzip2)
("python-screed" ,python-screed)
- ("python-bz2file" ,python-bz2file)
- ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
- ;; until the next version of khmer (likely 2.1) is released.
- ("gcc" ,gcc-4.9)))
+ ("python-bz2file" ,python-bz2file)))
(home-page "https://khmer.readthedocs.org/")
(synopsis "K-mer counting, filtering and graph traversal library")
(description "The khmer software is a set of command-line tools for
@@ -5601,25 +5576,38 @@ complexity samples.")
(define-public python-screed
(package
(name "python-screed")
- (version "0.9")
+ (version "1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "screed" version))
(sha256
(base32
- "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
+ "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ '(#:phases
(modify-phases %standard-phases
- (replace 'check
- (lambda _
- (setenv "PYTHONPATH"
- (string-append (getenv "PYTHONPATH") ":."))
- (zero? (system* "nosetests" "--attr" "!known_failing")))))))
+ ;; Tests must be run after installation, as the "screed" command does
+ ;; not exist right after building.
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (setenv "PYTHONPATH"
+ (string-append out "/lib/python"
+ (string-take (string-take-right
+ (assoc-ref inputs "python")
+ 5) 3)
+ "/site-packages:"
+ (getenv "PYTHONPATH")))
+ (setenv "PATH" (string-append out "/bin:" (getenv "PATH"))))
+ (invoke "python" "setup.py" "test")
+ #t)))))
(native-inputs
- `(("python-nose" ,python-nose)))
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-runner" ,python-pytest-runner)))
(inputs
`(("python-bz2file" ,python-bz2file)))
(home-page "https://github.com/dib-lab/screed/")
@@ -5746,14 +5734,15 @@ writing files into the .sra format.")
(define-public seqan
(package
(name "seqan")
- (version "1.4.2")
+ (version "2.4.0")
(source (origin
(method url-fetch)
- (uri (string-append "http://packages.seqan.de/seqan-library/"
- "seqan-library-" version ".tar.bz2"))
+ (uri (string-append "https://github.com/seqan/seqan/releases/"
+ "download/seqan-v" version
+ "/seqan-library-" version ".tar.xz"))
(sha256
(base32
- "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
+ "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
;; makes sense to split the outputs.
(outputs '("out" "doc"))
@@ -5763,11 +5752,11 @@ writing files into the .sra format.")
#:builder
(begin
(use-modules (guix build utils))
- (let ((tar (assoc-ref %build-inputs "tar"))
- (bzip (assoc-ref %build-inputs "bzip2"))
- (out (assoc-ref %outputs "out"))
- (doc (assoc-ref %outputs "doc")))
- (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
+ (let ((tar (assoc-ref %build-inputs "tar"))
+ (xz (assoc-ref %build-inputs "xz"))
+ (out (assoc-ref %outputs "out"))
+ (doc (assoc-ref %outputs "doc")))
+ (setenv "PATH" (string-append tar "/bin:" xz "/bin"))
(invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
(chdir (string-append "seqan-library-" ,version))
(copy-recursively "include" (string-append out "/include"))
@@ -5776,7 +5765,7 @@ writing files into the .sra format.")
(native-inputs
`(("source" ,source)
("tar" ,tar)
- ("bzip2" ,bzip2)))
+ ("xz" ,xz)))
(home-page "http://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
@@ -5787,6 +5776,41 @@ manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
+(define-public seqan-1
+ (package (inherit seqan)
+ (name "seqan")
+ (version "1.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://packages.seqan.de/seqan-library/"
+ "seqan-library-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
+ ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
+ ;; makes sense to split the outputs.
+ (outputs '("out" "doc"))
+ (build-system trivial-build-system)
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let ((tar (assoc-ref %build-inputs "tar"))
+ (bzip (assoc-ref %build-inputs "bzip2"))
+ (out (assoc-ref %outputs "out"))
+ (doc (assoc-ref %outputs "doc")))
+ (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
+ (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+ (chdir (string-append "seqan-library-" ,version))
+ (copy-recursively "include" (string-append out "/include"))
+ (copy-recursively "share" (string-append doc "/share"))
+ #t))))
+ (native-inputs
+ `(("source" ,source)
+ ("tar" ,tar)
+ ("bzip2" ,bzip2)))))
+
(define-public seqmagick
(package
(name "seqmagick")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 8fcf128135..e1f640ea85 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -98,6 +99,63 @@ it is easy to re-run the compilation with alternate programs. Bear is used to
generate such a compilation database.")
(license license:gpl3+)))
+(define-public gn
+ (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d")
+ (revision "1481")) ;as returned by `git describe`, used below
+ (package
+ (name "gn")
+ (version (git-version "0.0" revision commit))
+ (home-page "https://gn.googlesource.com/gn")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit commit)))
+ (sha256
+ (base32
+ "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d"))
+ (file-name (git-file-name name version))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;FIXME: How to run?
+ #:phases (modify-phases %standard-phases
+ (add-before 'configure 'set-build-environment
+ (lambda _
+ (setenv "CC" "gcc") (setenv "CXX" "g++")
+ (setenv "AR" "ar")
+ #t))
+ (replace 'configure
+ (lambda _
+ (invoke "python" "build/gen.py" "--no-sysroot"
+ "--no-last-commit-position")))
+ (add-after 'configure 'create-last-commit-position
+ (lambda _
+ ;; Create "last_commit_position.h" to avoid a dependency
+ ;; on 'git' (and the checkout..).
+ (call-with-output-file "out/last_commit_position.h"
+ (lambda (port)
+ (format port
+ "#define LAST_COMMIT_POSITION \"~a (~a)\"\n"
+ ,revision ,(string-take commit 8))
+ #t))))
+ (replace 'build
+ (lambda _
+ (invoke "ninja" "-C" "out" "gn"
+ "-j" (number->string (parallel-job-count)))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "out/gn" (string-append out "/bin"))
+ #t))))))
+ (native-inputs
+ `(("ninja" ,ninja)
+ ("python" ,python-2)))
+ (synopsis "Generate Ninja build files")
+ (description
+ "GN is a tool that collects information about a project from @file{.gn}
+files and generates build instructions for the Ninja build system.")
+ ;; GN is distributed as BSD-3, but bundles some files from ICU using the
+ ;; X11 license.
+ (license (list license:bsd-3 license:x11)))))
+
(define-public meson
(package
(name "meson")
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 77b4dba6d4..29d9a3d6ab 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -94,7 +94,7 @@ communication, encryption, decryption, signatures, etc.")
(define-public libmd
(package
(name "libmd")
- (version "1.0.0")
+ (version "1.0.1")
(source (origin
(method url-fetch)
(uri
@@ -105,7 +105,7 @@ communication, encryption, decryption, signatures, etc.")
version ".tar.xz")))
(sha256
(base32
- "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj"))))
+ "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1"))))
(build-system gnu-build-system)
(synopsis "Message Digest functions from BSD systems")
(description
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index ad1a8638bc..1dcf73771b 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -569,14 +569,14 @@ Extensions} (DNSSEC).")
(define-public knot
(package
(name "knot")
- (version "2.7.2")
+ (version "2.7.3")
(source (origin
(method url-fetch)
(uri (string-append "https://secure.nic.cz/files/knot-dns/"
name "-" version ".tar.xz"))
(sha256
(base32
- "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b"))
+ "1pwjcv7hzhqawisibybma160k77a6f1v94xw6ay9c7j49vrw05w7"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 8b02adc182..b333bb9d35 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -243,17 +243,17 @@ easy.")
(define-public snap
(package
(name "snap")
- (version "4.2.1.4")
+ (version "4.2.2.2")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jmoenig/Snap--Build-Your-Own-Blocks.git")
+ (url "https://github.com/jmoenig/Snap.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj"))))
+ "0bay08yr58qj8wzpjg33gdj78rfhyskfzidknpdl3cr1jrj6i4p9"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
@@ -265,7 +265,7 @@ easy.")
(share (string-append out "/share/snap")))
(copy-recursively source share)
;; Replace the sole minified file in the package.
- (with-directory-excursion share
+ (with-directory-excursion (string-append share "/src")
(delete-file "FileSaver.min.js")
(symlink (string-append (assoc-ref %build-inputs "js-filesaver")
"/share/javascript/FileSaver.min.js")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1069b9e3c3..ce98dbaeb8 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6,7 +6,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Chris Marusich <cmmarusich@gmail.com>
-;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
+;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber <cwebber@dustycloud.org>
;;; Copyright © 2016 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 David Thompson <davet@gnu.org>
@@ -654,6 +654,33 @@ Gitlab APIs from Emacs packages. It abstracts access to API resources using
only a handful of functions that are not resource-specific.")
(license license:gpl3+)))
+(define-public emacs-scribble-mode
+ (let ((commit "34e9e5edb921813b6483e0fefa848efb6ee4b314")
+ (version "0.0")
+ (revision 0))
+ (package
+ (name "emacs-scribble-mode")
+ (version (if (zero? revision)
+ version
+ (string-append version "-"
+ (number->string revision)
+ "." (string-take commit 7))))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/emacs-pe/scribble-mode.git")
+ (commit commit)))
+ (sha256
+ (base32
+ "0598byqpz2q6yi2q4dwd77jj9z3n99z34d3an51s9m2za0nh1qvp"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/emacs-pe/scribble-mode")
+ (synopsis "Emacs mode for editing the Scribble documentation syntax.")
+ (description
+ "This package provides basic syntax highlighting and editing support
+for editing Racket's Scribble documentation syntax in Emacs.")
+ (license license:gpl3+))))
+
(define-public emacs-haskell-mode
(package
(name "emacs-haskell-mode")
@@ -12386,3 +12413,23 @@ have special meaning. It is also handy for aligning text across long vertical
distances. Multi-column characters, such as @kbd{TAB} are treated
correctly.")
(license license:gpl2+)))
+
+(define-public emacs-slime-repl-ansi-color
+ (let ((commit "ad03263f5d4de473bc173b64a6fc3dc1106393d7"))
+ (package
+ (name "emacs-slime-repl-ansi-color")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deadtrickster/slime-repl-ansi-color")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0bpg7gxz310x7bnlg324c507sxc5gxwwz6h64h6kdq141r73vbi4"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/deadtrickster/slime-repl-ansi-color")
+ (synopsis "Color ANSI codes in the REPL of SLIME")
+ (description "Color ANSI codes in the REPL of SLIME")
+ (license license:gpl2+))))
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index ba37d6afa4..d4df84803b 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4098,15 +4098,15 @@ work and the interface is well tested.")
(define-public eolie
(package
(name "eolie")
- (version "0.9.38")
+ (version "0.9.45")
(source (origin
(method url-fetch)
(uri (string-append "https://gitlab.gnome.org/World/eolie/"
- "uploads/9814c06a1bc83ea09c3da8719a9ed11b/"
+ "uploads/020f3f686e2b938731752a1d9f5bfa7e/"
"eolie-" version ".tar.xz"))
(sha256
(base32
- "10vrh91rapgfmqwc6jkcybpmlvn4q0y8bnklw3rddzigf9kvqsff"))))
+ "0371p7g13r0b7zjc48fdcil43ddwpmyvkd2a4vv6ifsqmny6kl42"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index f058cc79a2..dd83a08038 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -30,6 +30,7 @@
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2018 Manuel Graf <graf@init.at>
+;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -399,8 +400,8 @@ It has been modified to remove all non-free binary blobs.")
;; supports qemu "virt" machine and possibly a large number of ARM boards.
;; See : https://wiki.debian.org/DebianKernel/ARMMP.
-(define %linux-libre-version "4.18.15")
-(define %linux-libre-hash "0v6xs85qn1iy2dj3m6s3cfnhbwb1mjy21d9lagjni8dg3jic26hf")
+(define %linux-libre-version "4.18.16")
+(define %linux-libre-hash "15apfgswp2lrwjpi3vwnanlkdw3q6rkvwrbgrb71rjsy9gazlz62")
(define %linux-libre-4.18-patches
(list %boot-logo-patch
@@ -430,8 +431,8 @@ It has been modified to remove all non-free binary blobs.")
#:patches %linux-libre-4.18-patches
#:configuration-file kernel-config))
-(define %linux-libre-4.14-version "4.14.77")
-(define %linux-libre-4.14-hash "18y81rga2lhsk7bjckglxz52pvnzf103ar0z2zj611g37wyf83r5")
+(define %linux-libre-4.14-version "4.14.78")
+(define %linux-libre-4.14-hash "07dhhw6zdnqn2dznpmkniz58hfkdx89yx7csm9vbx45blnyhjw5z")
(define-public linux-libre-4.14
(make-linux-libre %linux-libre-4.14-version
@@ -440,14 +441,14 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
- (make-linux-libre "4.9.134"
- "0f5qif27k0mhc57d98arbfkq7zlvg0ra2gz6g5fasblyjz3j7w7h"
+ (make-linux-libre "4.9.135"
+ "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
- (make-linux-libre "4.4.161"
- "1q6bsndpjgw72mybhl5l8vrxs4mimg6821bjgi1pjkxbc7nd921b"
+ (make-linux-libre "4.4.162"
+ "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2"
%intel-compatible-systems
#:configuration-file kernel-config))
@@ -4167,30 +4168,21 @@ monitoring tools for Linux. These include @code{mpstat}, @code{iostat},
(define-public light
(package
(name "light")
- (version "1.1.2")
+ (version "1.2")
(source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/haikarainen/light")
- (commit version)))
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/haikarainen/light/archive/v"
+ version ".tar.gz"))
(sha256
(base32
- "0c934gxav9cgdf94li6dp0rfqmpday9d33vdn9xb2mfp4war9n4w"))))
+ "1gfvsw7gh5pis733l7j54vzp272pvjyzbg8a0pvapfmg0s7mip97"))
+ (file-name (string-append name "-" version ".tar.gz"))))
(build-system gnu-build-system)
- (arguments
- '(#:tests? #f ; no tests
- #:make-flags (list "CC=gcc"
- (string-append "PREFIX=" %output))
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; no configure script
- (add-after 'unpack 'patch-makefile
- (lambda _
- (substitute* "Makefile" (("chown") "#"))
- #t)))))
(native-inputs
- `(("help2man" ,help2man)))
- (home-page "https://haikarainen.github.io/light")
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)))
+ (home-page "https://haikarainen.github.io/light/")
(synopsis "GNU/Linux application to control backlights")
(description
"Light is a program to send commands to screen backlight controllers
diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm