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| author | Timothy Sample <samplet@ngyro.com> | 2019-11-13 22:59:24 -0500 |
|---|---|---|
| committer | Timothy Sample <samplet@ngyro.com> | 2019-11-20 20:48:54 -0500 |
| commit | c1637311b6331588734791a87376023338b6a4a3 (patch) | |
| tree | 227ec8c1d95f4a6337941bf6440ccdd78a63d9b3 | |
| parent | 74be1cb7b4780d32485848d7e121d05e0aaa670e (diff) | |
| download | patches-c1637311b6331588734791a87376023338b6a4a3.tar patches-c1637311b6331588734791a87376023338b6a4a3.tar.gz | |
gnu: ngless: Update to 1.0.1.
* gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1.
[arguments]: Add a 'create-Versions.hs' phase that patches the Makefile
and invokes 'make' to generate a required file.
[inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and
'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib',
'ghc-diagrams-svg', and 'ghc-tar-conduit'.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 30 |
1 files changed, 24 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 07c70fb82c..511146bb6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13890,7 +13890,7 @@ datasets.") (define-public ngless (package (name "ngless") - (version "0.9.1") + (version "1.0.1") (source (origin (method git-fetch) @@ -13900,7 +13900,7 @@ datasets.") (file-name (git-file-name name version)) (sha256 (base32 - "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117")))) + "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg")))) (build-system haskell-build-system) (arguments `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: @@ -13908,7 +13908,24 @@ datasets.") ; import Options.Applicative #:phases (modify-phases %standard-phases - (add-after 'unpack 'create-cabal-file + (add-after 'unpack 'create-Versions.hs + (lambda _ + (substitute* "Makefile" + (("BWA_VERSION = .*") + (string-append "BWA_VERSION = " + ,(package-version bwa) "\n")) + (("SAM_VERSION = .*") + (string-append "SAM_VERSION = " + ,(package-version samtools) "\n")) + (("PRODIGAL_VERSION = .*") + (string-append "PRODIGAL_VERSION = " + ,(package-version prodigal) "\n")) + (("MINIMAP2_VERSION = .*") + (string-append "MINIMAP2_VERSION = " + ,(package-version minimap2) "\n"))) + (invoke "make" "NGLess/Dependencies/Versions.hs") + #t)) + (add-after 'create-Versions.hs 'create-cabal-file (lambda _ (invoke "hpack") #t)) ;; These tools are expected to be installed alongside ngless. (add-after 'install 'link-tools @@ -13937,15 +13954,15 @@ datasets.") ("ghc-async" ,ghc-async) ("ghc-atomic-write" ,ghc-atomic-write) ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) - ("ghc-chart" ,ghc-chart) - ("ghc-chart-cairo" ,ghc-chart-cairo) ("ghc-conduit" ,ghc-conduit) ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) - ("ghc-conduit-combinators" ,ghc-conduit-combinators) ("ghc-conduit-extra" ,ghc-conduit-extra) ("ghc-configurator" ,ghc-configurator) ("ghc-convertible" ,ghc-convertible) ("ghc-data-default" ,ghc-data-default) + ("ghc-diagrams-core" ,ghc-diagrams-core) + ("ghc-diagrams-lib" ,ghc-diagrams-lib) + ("ghc-diagrams-svg" ,ghc-diagrams-svg) ("ghc-double-conversion" ,ghc-double-conversion) ("ghc-edit-distance" ,ghc-edit-distance) ("ghc-either" ,ghc-either) @@ -13966,6 +13983,7 @@ datasets.") ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) + ("ghc-tar-conduit" ,ghc-tar-conduit) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) |