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2020-02-26gnu: proteinortho: Update to 6.0.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14. [source]: Fetch from git; remove pre-built scripts. [arguments]: Set make-flags; update wrap-programs phase to wrap all scripts. [inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove python-2. [native-inputs]: Add which. [license]: Update to GPLv3+
2020-02-26gnu: diamond: Update to 0.9.30.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
2020-02-26gnu: crossmap: Update to 0.3.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8. [arguments]: Remove to build with default Python. [inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and python2-pysam with their Python 3 variants. [native-inputs]: Replace python2-cython and python2-nose with their Python 3 variants.
2020-02-26gnu: Add rust-libressl-pnacl-sys-2.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-libressl-pnacl-sys-2): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-pnacl-build-helper-1.4.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-pnacl-build-helper-1.4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-zip-0.5.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-zip-0.5): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-bzip2-0.3.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-bzip2-0.3): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-partial-io-0.2.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-partial-io-0.2): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-winpty-sys-0.4.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-winpty-sys-0.4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-bindgen-0.33.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-bindgen-0.33): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-cexpr-0.2.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-cexpr-0.2): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-clang-sys-0.11.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-clang-sys-0.11): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-libloading-0.3.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-libloading-0.3): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-target-build-utils-0.3.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-target-build-utils-0.3): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-json-0.9.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-json-0.9): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-linked-hash-map-0.4.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-linked-hash-map-0.4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-macros-0.4.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-macros-0.4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-test-0.9.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-test-0.9): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-0.4.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-0.4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-0.9.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-0.9): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-derive-0.9.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-derive-0.9): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: Add rust-serde-codegen-internals-0.14.Valentin Ignatev
* gnu/packages/crates-io.scm (rust-serde-codegen-internals-0.14): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-02-26gnu: macs: Update to 2.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6. [source]: Fetch from git. [arguments]: Enable tests, build with default Python. [inputs]: Replace python2-numpy with python-numpy. [native-inputs]: Add python-pytest.
2020-02-26gnu: Add cl-dbd-sqlite3.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-dbd-sqlite3, cl-dbd-sqlite3): New variables.
2020-02-26gnu: Add cl-dbd-postgres.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-dbd-postgres, cl-dbd-postgres): New variables.
2020-02-26gnu: Add cl-dbd-mysql.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-dbd-mysql, cl-dbd-mysql): New variables.
2020-02-26gnu: Add cl-dbi.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-dbi, cl-dbi): New variables.
2020-02-26gnu: Add cl-postmodern.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-postmodern, cl-postmodern): New variables.
2020-02-26gnu: Add cl-s-sql.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-s-sql, cl-s-sql): New variables.
2020-02-26gnu: Add cl-simple-date-postgres-glue.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-simple-date-postgres-glue, cl-simple-date-postgres-glue): New variables.
2020-02-26gnu: Add cl-postgres.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-cl-postgres, cl-postgres): New variables.
2020-02-26gnu: Add cl-simple-date.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-simple-date, cl-simple-date, ecl-simple-date): New variables.
2020-02-26gnu: Add cl-mysql.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-cl-mysql, cl-mysql): New variables.
2020-02-26gnu: Add r-rstanarm.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstanarm): New variable.
2020-02-26gnu: Add r-rstan.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstan): New variable.
2020-02-26gnu: Add r-loo.Ricardo Wurmus
* gnu/packages/cran.scm (r-loo): New variable.
2020-02-26gnu: Add r-rstantools.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstantools): New variable.
2020-02-26gnu: Add r-shinystan.Ricardo Wurmus
* gnu/packages/cran.scm (r-shinystan): New variable.
2020-02-26gnu: Add r-dygraphs.Ricardo Wurmus
* gnu/packages/cran.scm (r-dygraphs): New variable.
2020-02-26gnu: Remove python-loompy-for-pigx-scrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable.
2020-02-26gnu: pigx-scrnaseq: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3. [arguments]: Remove. [inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
2020-02-25gnu: clang-runtime-3.5: Fix build.Ricardo Wurmus
* gnu/packages/llvm.scm (clang-runtime-3.5) [inputs]: Add libtirpc. [arguments]: Add phase to find rpc headers.
2020-02-25gnu: Add r-rsconnect.Ricardo Wurmus
* gnu/packages/cran.scm (r-rsconnect): New variable.
2020-02-25gnu: Add r-packrat.Ricardo Wurmus
* gnu/packages/cran.scm (r-packrat): New variable.
2020-02-25gnu: zrythm: Update to 0.7.573.Alexandros Theodotou
* gnu/packages/music.scm (zrythm): Update to 0.7.573. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
2020-02-25gnu: libzip: Update to 1.6.1.Marius Bakke
* gnu/packages/compression.scm (libzip): Update to 1.6.1. [inputs]: Add XZ.
2020-02-25gnu: python-xmlschema: Update to 1.1.1.Marius Bakke
* gnu/packages/xml.scm (python-xmlschema): Update to 1.1.1.
2020-02-25gnu: xapian: Update to 1.4.15.Marius Bakke
* gnu/packages/search.scm (xapian, python-xapian-bindings): Update to 1.4.15.
2020-02-25gnu: libgphoto2: Update to 2.5.24.Marius Bakke
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.24.
2020-02-25gnu: fluidsynth: Update to 2.1.1.Marius Bakke
* gnu/packages/audio.scm (fluidsynth): Update to 2.1.1.
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