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* gnu: r-delayedmatrixstats: Update to 1.6.1.Ricardo Wurmus2019-09-14
| | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
* gnu: r-rhdf5lib: Update to 1.6.1.Ricardo Wurmus2019-09-14
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
* gnu: r-rtracklayer: Update to 1.44.4.Ricardo Wurmus2019-09-14
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
* gnu: r-genomicranges: Update to 1.36.1.Ricardo Wurmus2019-09-14
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
* gnu: r-s4vectors: Update to 0.22.1.Ricardo Wurmus2019-09-14
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
* gnu: r-gprofiler: Update to 0.6.8.Ricardo Wurmus2019-09-08
| | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
* gnu: r-annotationhub: Update to 2.16.1.Ricardo Wurmus2019-09-08
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
* gnu: r-edger: Update to 3.26.8.Ricardo Wurmus2019-09-08
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
* gnu: Add samblaster.Ricardo Wurmus2019-09-06
| | | | * gnu/packages/bioinformatics.scm (samblaster): New variable.
* gnu: libbigwig: Update to 0.4.4.Ricardo Wurmus2019-09-05
| | | | * gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
* gnu: python-pyfaidx: Remove python-setuptools as an input.Christopher Baines2019-09-05
| | | | | | | | As this is provided by the build system, and I'm assuming that it's not necessary to have it as a propagated input. * gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove python-setuptools.
* gnu: umi-tools: Remove python-setuptools as an input.Christopher Baines2019-09-05
| | | | | | | As this is provided by the build system. * gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove python-setuptools.
* gnu: bwa-meth: Capture one more reference to "bwa".Ricardo Wurmus2019-09-05
| | | | | | | Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de> * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of "bwa index" to retain reference to "bwa" package.
* gnu: r-ldblock: Update to 1.14.2.Ricardo Wurmus2019-09-02
| | | | | | * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2. [propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and r-httr.
* gnu: r-seurat: Update to 3.1.0.Ricardo Wurmus2019-09-02
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0. [propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot.
* gnu: r-rtracklayer: Update to 1.44.3.Ricardo Wurmus2019-09-02
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3.
* gnu: r-biomart: Update to 2.40.4.Ricardo Wurmus2019-09-02
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4.
* gnu: r-annotationdbi: Update to 1.46.1.Ricardo Wurmus2019-09-02
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1.
* gnu: r-iranges: Update to 2.18.2.Ricardo Wurmus2019-09-02
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2.
* gnu: Move non-compilers out of haskell.scm.Robert Vollmert2019-08-31
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/haskell.scm (ghc-abstract-deque, ghc-abstract-par, ghc-adjunctions, ghc-aeson-compat, ghc-alex, ghc-alsa-core, ghc-annotated-wl-pprint, ghc-ansi-terminal, ghc-ansi-wl-pprint, ghc-appar, ghc-async, ghc-atomic-write, ghc-attoparsec, ghc-attoparsec-bootstrap, ghc-attoparsec-iso8601, ghc-auto-update, ghc-aws, ghc-base16-bytestring, ghc-base64-bytestring, ghc-base-compat, ghc-basement, ghc-base-orphans, ghc-base-prelude, ghc-base-unicode-symbols, ghc-bifunctors, ghc-bindings-dsl, ghc-blaze-builder, ghc-blaze-markup, ghc-bloomfilter, ghc-boxes, ghc-byteable, ghc-byteorder, ghc-bytes, ghc-bytestring-builder, ghc-bytestring-handle, ghc-bytestring-lexing, ghc-bzlib-conduit, ghc-c2hs, ghc-cairo, ghc-call-stack, ghc-call-stack-boot, ghc-case-insensitive, ghc-cereal, ghc-cereal-conduit, ghc-cgi, ghc-charset, ghc-chart, ghc-chart-cairo, ghc-chasingbottoms, ghc-cheapskate, ghc-chell, ghc-chell-quickcheck, ghc-chunked-data, ghc-clock, ghc-clock-bootstrap, ghc-cmark, ghc-cmark-gfm, ghc-cmdargs, ghc-code-page, ghc-colour, ghc-comonad, ghc-concatenative, ghc-concurrent-output, ghc-conduit, ghc-conduit-algorithms, ghc-conduit-combinators, ghc-conduit-extra, ghc-configurator, ghc-connection, ghc-constraints, ghc-contravariant, ghc-contravariant-extras, ghc-convertible, ghc-data-accessor, ghc-data-accessor-transformers, ghc-data-default, ghc-data-default-class, ghc-data-default-instances-base, ghc-data-default-instances-containers, ghc-data-default-instances-dlist, ghc-data-default-instances-old-locale, ghc-data-hash, ghc-data-ordlist, ghc-deepseq-generics, ghc-descriptive, ghc-diff, ghc-disk-free-space, ghc-distributive, ghc-dlist, ghc-doctemplates, ghc-doctest, ghc-double-conversion, ghc-easy-file, ghc-easyplot, ghc-echo, ghc-edisonapi, ghc-edisoncore, ghc-edit-distance, ghc-either, ghc-email-validate, ghc-enclosed-exceptions, ghc-equivalence, ghc-erf, ghc-errorcall-eq-instance, ghc-errors, ghc-esqueleto, ghc-exactprint, ghc-exceptions, ghc-executable-path, ghc-extensible-exceptions, ghc-extra, ghc-fail, ghc-fast-logger, ghc-feed, ghc-fgl, ghc-fgl-arbitrary, ghc-file-embed, ghc-filemanip, ghc-findbin, ghc-fingertree, ghc-fixed, ghc-foldl, ghc-foundation, ghc-free, ghc-fsnotify, ghc-generic-deriving, ghc-generics-sop, ghc-geniplate-mirror, ghc-genvalidity, ghc-genvalidity-property, ghc-gitrev, ghc-glob, ghc-gluraw, ghc-glut, ghc-gnuplot, ghc-graphviz, ghc-gtk2hs-buildtools, ghc-hackage-security, ghc-haddock, ghc-haddock-api, ghc-haddock-library, ghc-half, ghc-happy, ghc-hashable, ghc-hashable-bootstrap, ghc-hashable-time, ghc-hashtables, ghc-haskell-lexer, ghc-haskell-src, ghc-haskell-src-exts, ghc-haskell-src-exts-util, ghc-haskell-src-meta, ghc-hasktags, ghc-hex, ghc-highlighting-kate, ghc-hindent, ghc-hinotify, ghc-hmatrix, ghc-hmatrix-gsl, ghc-hmatrix-gsl-stats, ghc-hmatrix-special, ghc-hostname, ghc-hourglass, ghc-hpack, ghc-hs-bibutils, ghc-hslogger, ghc-hslua, ghc-hslua-module-text, ghc-http-api-data, ghc-ieee754, ghc-ifelse, ghc-indents, ghc-inline-c, ghc-inline-c-cpp, ghc-integer-logarithms, ghc-integer-logarithms-bootstrap, ghc-interpolate, ghc-intervalmap, ghc-invariant, ghc-iproute, ghc-iwlib, ghc-json, ghc-juicypixels, ghc-kan-extensions, ghc-language-c, ghc-language-haskell-extract, ghc-lens, ghc-libffi, ghc-libmpd, ghc-libxml, ghc-lifted-async, ghc-lifted-base, ghc-linear, ghc-logging-facade, ghc-logict, ghc-lzma, ghc-lzma-conduit, ghc-markdown-unlit, ghc-math-functions, ghc-megaparsec, ghc-memory, ghc-memotrie, ghc-microlens, ghc-microlens-ghc, ghc-microlens-mtl, ghc-microlens-platform, ghc-microlens-th, ghc-missingh, ghc-mmap, ghc-mmorph, ghc-mockery, ghc-monad-control, ghc-monad-logger, ghc-monad-loops, ghc-monad-par, ghc-monad-par-extras, ghc-monadplus, ghc-monadrandom, ghc-monads-tf, ghc-mono-traversable, ghc-murmur-hash, ghc-mwc-random, ghc-nats, ghc-nats-bootstrap, ghc-network, ghc-network-info, ghc-network-uri, ghc-newtype-generics, ghc-objectname, ghc-old-locale, ghc-old-time, ghc-opengl, ghc-openglraw, ghc-operational, ghc-options, ghc-optparse-applicative, ghc-pandoc, ghc-pandoc-citeproc, ghc-pandoc-types, ghc-parallel, ghc-parsec-numbers, ghc-parser-combinators, ghc-parsers, ghc-path, ghc-path-io, ghc-paths, ghc-patience, ghc-pcre-light, ghc-persistent, ghc-persistent-sqlite, ghc-persistent-template, ghc-polyparse, ghc-pqueue, ghc-prelude-extras, ghc-pretty-hex, ghc-pretty-show, ghc-primitive, ghc-profunctors, ghc-psqueues, ghc-random, ghc-raw-strings-qq, ghc-rebase, ghc-reducers, ghc-refact, ghc-reflection, ghc-regex, ghc-regex-applicative, ghc-regex-base, ghc-regex-compat, ghc-regex-compat-tdfa, ghc-regex-pcre-builtin, ghc-regex-posix, ghc-regex-tdfa, ghc-regex-tdfa-text, ghc-rerebase, ghc-resolv, ghc-resource-pool, ghc-resourcet, ghc-rfc5051, ghc-rio, ghc-safe, ghc-safe-exceptions, ghc-safeio, ghc-safesemaphore, ghc-sandi, ghc-scientific, ghc-scientific-bootstrap, ghc-sdl, ghc-sdl-image, ghc-sdl-mixer, ghc-securemem, ghc-semigroupoids, ghc-semigroups, ghc-semigroups-bootstrap, ghc-setenv, ghc-setlocale, ghc-shakespeare, ghc-shelly, ghc-silently, ghc-simple-reflect, ghc-simple-sendfile, ghc-skylighting-core, ghc-skylighting, ghc-smallcheck, ghc-socks, ghc-split, ghc-statevar, ghc-statistics, ghc-stm-chans, ghc-stm-conduit, ghc-stmonadtrans, ghc-storable-complex, ghc-streaming-commons, ghc-strict, ghc-stringbuilder, ghc-string-qq, ghc-stringsearch, ghc-stylish-haskell, ghc-syb, ghc-system-fileio, ghc-system-filepath, ghc-tagged, ghc-tar, ghc-temporary, ghc-temporary-rc, ghc-terminal-size, ghc-texmath, ghc-text-binary, ghc-tf-random, ghc-th-abstraction, ghc-th-expand-syns, ghc-th-lift, ghc-th-lift-instances, ghc-th-orphans, ghc-th-reify-many, ghc-time-locale-compat, ghc-tldr, ghc-transformers-base, ghc-transformers-compat, ghc-tree-diff, ghc-trifecta, ghc-tuple-th, ghc-typed-process, ghc-unbounded-delays, ghc-unexceptionalio, ghc-union-find, ghc-uniplate, ghc-unix-compat, ghc-unix-time, ghc-unliftio, ghc-unliftio-core, ghc-unordered-containers, ghc-unordered-containers-bootstrap, ghc-uri-bytestring, ghc-utf8-string, ghc-utility-ht, ghc-uuid, ghc-uuid-types, ghc-validation, ghc-validity, ghc-vault, ghc-vector, ghc-vector-algorithms, ghc-vector-binary-instances, ghc-vector-builder, ghc-vector-th-unbox, ghc-void, ghc-wave, ghc-wcwidth, ghc-wcwidth-bootstrap, ghc-weigh, ghc-wl-pprint, ghc-wl-pprint-annotated, ghc-wl-pprint-text, ghc-word8, ghc-x11, ghc-x11-xft, ghc-xdg-basedir, ghc-xml, ghc-xml-conduit, ghc-xml-types, ghc-yaml, ghc-zip-archive, ghc-zlib): Move variables from here... * gnu/packages/haskell-xyz.scm: ...to here. * gnu/packages/agda.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/cran.scm, gnu/packages/emacs-xyz.scm, gnu/packages/games.scm, gnu/packages/graphics.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-check.scm, gnu/packages/idris.scm, gnu/packages/statistics.scm, gnu/packages/wm.scm: Update module references. Co-authored-by: Timothy Sample <samplet@ngyro.com>
* gnu: edirect: Update to 12.1.20190819.Efraim Flashner2019-08-20
| | | | * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819.
* gnu: r-gviz: Update to 1.28.1.Ricardo Wurmus2019-08-19
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1.
* gnu: r-edger: Update to 3.26.7.Ricardo Wurmus2019-08-16
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.7.
* gnu: freebayes: Simplify and enable tests.Ricardo Wurmus2019-08-09
| | | | | | | | * gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles" phase; move build of tabixpp and vcflib to separate phase "build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build" phase.
* gnu: freebayes: Move bamtools to inputs.Ricardo Wurmus2019-08-09
| | | | | | * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools from here... [inputs]: ...to here.
* gnu: Add freebayes.Pierre Neidhardt2019-08-09
| | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
* gnu: Add vcflib.Pierre Neidhardt2019-08-09
| | | | | * gnu/packages/bioinformatics.scm (vcflib): New variable. (tabixpp-freebayes): New private variable.
* gnu: r-hdf5array: Update to 1.12.2.Ricardo Wurmus2019-08-08
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
* gnu: r-biocparallel: Update to 1.18.1.Ricardo Wurmus2019-08-08
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
* Revert "gnu: Add vcflib."Efraim Flashner2019-08-08
| | | | | | This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master
* Revert "gnu: Add freebayes."Efraim Flashner2019-08-08
| | | | This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
* gnu: Add freebayes.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
* gnu: Add vcflib.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (vcflib): New variable.
* gnu: Add fastahack.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (fastahack): New variable.
* gnu: Add fsom.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (fsom): New variable.
* gnu: Add multichoose.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (multichoose): New variable.
* gnu: Add smithwaterman.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (smithwaterman): New variable.
* gnu: Add tabixpp.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (tabixpp): New variable.
* gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml.Robert Vollmert2019-08-07
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | These are ghc-8.4-bundled packages, removing to avoid build conflicts. * gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove. * gnu/packages/haskell-web.scm (ghc-xhtml): Remove. * gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text. * gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and ghc-text. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec. (git-annex)[inputs]: Remove ghc-stm and ghc-text. (ghc-sdl2)[inputs]: Remove ghc-text. (ghc-sdl2-image)[inputs]: Remove ghc-text. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm. (ghc-tasty)[inputs]: Remove ghc-stm. (ghc-tasty-rerun)[inputs]: Same. (ghc-quickcheck-instances)[inputs]: Remove ghc-text. (ghc-hedgehog)[inputs]: Remove ghc-stm. * gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove ghc-text. * gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text. (ghc-cookie)[inputs]: Same. (ghc-http-types)[inputs]: Same. (ghc-http)[inputs]: Remove ghc-parsec. (ghc-http-client)[inputs]: Remove ghc-text. (ghc-http2)[inputs]: Remove ghc-stm. (ghc-http-conduit)[native-inputs]: Remove ghc-text. (ghc-wai)[inputs]: Same. (ghc-wai-extra)[inputs]: Same. (ghc-warp)[inputs]: Remove ghc-stm and ghc-text. (ghc-xss-sanitize)[native-inputs]: Remove ghc-text. (ghc-css-text)[inputs]: Same. (ghc-mime-types)[inputs]: Same. (ghc-blaze-html)[inputs]: Same. (ghc-aeson)[inputs]: Same. (ghc-aeson-pretty)[inputs]: Same. (ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec. (ghc-multipart)[inputs]: Remove ghc-parsec. (ghc-uri-encode)[inputs]: Remove ghc-text. (ghc-path-pieces)[inputs]: Same. (ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec. (ghc-yesod-persistent)[inputs]: Remove ghc-text. (ghc-yesod-form)[inputs]: Same. (ghc-yesod)[inputs]: Same. (ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text. (ghc-hxt)[inputs]: Remove ghc-parsec. * gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text. (ghc-double-conversion)[inputs]: Same. (ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text. [native-inputs]: Remove ghc-parsec. (ghc-cgi)[inputs]: Remove ghc-parsec. (hlint)[inputs]: Remove ghc-text. (ghc-openglraw)[inputs]: Remove ghc-text. (ghc-opengl)[inputs]: Same. (ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text. (ghc-hackage-security)[inputs]: Remove ghc-parsec. (cabal-install)[inputs]: Remove ghc-stm. (ghc-parsec-numbers)[inputs]: Remove ghc-parsec. (ghc-safesemaphore)[inputs]: Remove ghc-stm. (ghc-text-binary)[inputs]: Remove ghc-text. (ghc-hashable)[inputs]: Remove ghc-text. (ghc-transformers-base)[inputs]: Remove ghc-stm. (ghc-indents)[inputs]: Remove ghc-parsec. (ghc-regex-tdfa-rc)[inputs]: Same. (ghc-regex-tdfa-text)[inputs]: Same. (ghc-regex)[inputs]: Remove ghc-text. (ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text. (ghc-attoparsec)[inputs]: Remove ghc-text. (ghc-attoparsec-bootstrap)[inputs]: Same. (ghc-zip-archive)[inputs]: Same. (ghc-polyparse)[inputs]: Same. (ghc-reducers)[inputs]: Same. (ghc-xml)[inputs]: Same. (ghc-feed)[inputs]: Same. (ghc-exceptions)[inputs]: Remove ghc-stm. (ghc-case-insensitive)[inputs]: Remove ghc-text. (ghc-megaparsec)[inputs]: Same. (ghc-network-uri)[inputs]: Remove ghc-parsec. (ghc-monad-control)[inputs]: Remove ghc-stm. (ghc-blaze-builder)[inputs]: Remove ghc-text. (ghc-blaze-markup)[inputs]: Same. (ghc-async)[inputs]: Remove ghc-stm. (ghc-invariant)[inputs]: Same. (ghc-statevar)[inputs]: Same. (ghc-lens)[inputs]: Remove ghc-text. (ghc-cheapskate)[inputs]: Same. (ghc-semigroups)[inputs]: Same. (ghc-semigroups-bootstrap)[inputs]: Same. (ghc-fast-logger)[inputs]: Same. (ghc-scientific)[inputs]: Same. (ghc-scientific-bootstrap)[inputs]: Same. (ghc-texmath)[inputs]: Remove ghc-parsec. (ghc-highlighting-kate)[inputs]: Same. (ghc-cmark)[inputs]: Remove ghc-text. (ghc-cmark-gfm)[inputs]: Same. (ghc-th-lift-instances)[inputs]: Same. (ghc-yaml)[inputs]: Same. (ghc-hslua)[inputs]: Same. (ghc-hslua-module-text)[inputs]: Same. (ghc-skylighting-core)[inputs]: Same. (ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec. (ghc-pandoc)[inputs]: Same. (ghc-typed-process)[inputs]: Remove ghc-stm. (ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text. (ghc-xml-types)[inputs]: Remove ghc-text. (ghc-xml-conduit)[inputs]: Same. (ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec. (ghc-regex-tdfa)[inputs]: Remove ghc-parsec. (ghc-wl-pprint-text)[inputs]: Remove ghc-text. (ghc-graphviz)[inputs]: Same. (ghc-system-filepath-bootstrap)[inputs]: Same. (ghc-system-fileio-bootstrap)[inputs]: Same. (ghc-shelly)[inputs]: Same. (ghc-chell)[inputs]: Same. (ghc-system-filepath)[inputs]: Same. (ghc-system-fileio)[inputs]: Same. (ghc-fsnotify)[inputs]: Same. (ghc-json)[inputs]: Remove ghc-text and ghc-parsec. (ghc-esqueleto)[inputs]: Remove ghc-text. (shellcheck)[inputs]: Remove ghc-parsec. (ghc-errors)[inputs]: Remove ghc-text. (ghc-chunked-data)[inputs]: Same. (ghc-uuid-types)[inputs]: Same. (ghc-uuid)[inputs]: Same. (ghc-rebase)[inputs]: Remove ghc-stm and ghc-text. (ghc-foldl)[inputs]: Remove ghc-text. (ghc-mono-traversable)[inputs]: Same. (ghc-conduit-combinators)[inputs]: Same. (ghc-aws)[inputs]: Same. (ghc-stm-chans)[inputs]: Remove ghc-stm. (ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm. (ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text. (ghc-resource-pool)[inputs]: Remove ghc-stm. (ghc-attoparsec-iso8601)[inputs]: Remove ghc-text. (ghc-http-api-data)[inputs]: Same. (ghc-persistent)[inputs]: Same. (ghc-aeson-compat)[inputs]: Same. (ghc-persistent-template)[inputs]: Same. (ghc-unliftio)[inputs]: Remove ghc-stm. (ghc-persistent-sqlite)[native-inputs]: Remove ghc-text. (ghc-bytes)[inputs]: Same. (ghc-missingh)[inputs]: Remove ghc-parsec. (ghc-rio)[inputs]: Remove ghc-text. (ghc-cairo)[inputs]: Same. (ghc-atomic-write)[inputs]: Remove ghc-text. [native-inputs]: Same. (ghc-stm-conduit)[inputs]: Remove ghc-stm. (ghc-conduit-algorithms)[inputs]: Same. (ghc-interpolate)[native-inputs]: Remove ghc-text. (ghc-hpack)[inputs]: Same. (ghc-inline-c)[inputs]: Remove ghc-parsec. (ghc-configurator)[inputs]: Remove ghc-text. (ghc-c2hs)[native-inputs]: Same. (ghc-libmpd)[inputs]: Same. (ghc-concurrent-output)[inputs]: Remove ghc-stm. * gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text. * gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: r-msnid: Update to 1.18.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
* gnu: r-rcas: Update to 1.10.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
* gnu: r-genomicfeatures: Update to 1.36.4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
* gnu: r-rtracklayer: Update to 1.44.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
* gnu: r-summarizedexperiment: Update to 1.14.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
* gnu: r-biomart: Update to 2.40.3.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
* gnu: r-limma: Update to 3.40.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
* gnu: r-edger: Update to 3.26.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
* gnu: khmer: Make gzip timestamps writable.Brian Leung2019-08-05
| | | | | | | * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase to make gzip timestamps writable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Explicitly refer to 'guile-json-1' when needed.Ludovic Courtès2019-07-25
| | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change 'guile-json' to 'guile-json-1'. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise. * gnu/packages/mail.scm (mumi)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise. * gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.
* gnu: htslib: Propagate zlib.Ricardo Wurmus2019-07-22
| | | | | | | Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here.
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-10 07:57:23 +0000