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zimoun
bd746917a2
gnu: julia-forwarddiff: Disable tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-forwarddiff)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:33 +02:00
zimoun
82586916be
gnu: julia-geometrybasics: Fix tests on i686-linux. 
* gnu/packages/julia-xyz (julia-geometrybasics)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:33 +02:00
zimoun
eb4f1fcf74
gnu: julia-structarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-structarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in the test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
afd35e8e9c
gnu: julia-mutablearithmetics: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
630824a238
gnu: julia-woodburymatrices: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-woodburymatrices)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
828012ed9f
gnu: julia-intervalsets: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-intervalsets)[arguments]<#:phases>:
Conditionally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:32 +02:00
zimoun
29c0410086
gnu: julia-reversediff: Disable tests on i686-linux. 
* gnu/packages/julia-xyz (julia-reversediff)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
28d530ea44
gnu: julia-interpolations: Disable tests in i686-linux. 
* gnu/packages/julia-xyz.scm (julia-interpolations)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
e3c15b0bfc
gnu: julia-arrayinterface: Disable tests for i686. 
* gnu/packages/julia-xyz.scm (julia-arrayinterface)[arguments]<#:tests?>:
Conditionally disable tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:31 +02:00
zimoun
7c8e9cbfa9
gnu: julia-mappedarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-mappedarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
dcd7c950c6
gnu: julia-blockarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-blockarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
557caa4e2c
gnu: julia-lazyarrays: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-lazyarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
dbad333481
gnu: julia-configurations: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-configurations)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:30 +02:00
zimoun
a31a4517b6
gnu: julia-finitedifferences: Fix tests on i686-linux. 
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
2a749f34e5
gnu: julia-benchmarktools: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
7fee8a46fb
gnu: julia-datastructures: Fix tests on i686-linux. 
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:50:29 +02:00
zimoun
9112bed608
gnu: libunwind-julia: Fix build on i686-linux. 
* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-04 19:33:30 +02:00
Ricardo Wurmus
cc491eab7e
gnu: plink-ng: Enable tests. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
 2021-12-04 16:00:08 +01:00
Ricardo Wurmus
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:35:28 +01:00
Ricardo Wurmus
88bb81b515
gnu: plink: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
 2021-12-04 15:31:31 +01:00
Ricardo Wurmus
e920101141
gnu: plink: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 15:31:08 +01:00
Ricardo Wurmus
a4e7475edc
gnu: rsem: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
 2021-12-04 15:27:39 +01:00
Ricardo Wurmus
c45c909026
gnu: rsem: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:26:48 +01:00
Ricardo Wurmus
5e0bcba57b
gnu: rsem: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
 2021-12-04 15:26:01 +01:00
Ricardo Wurmus
23975fe27a
gnu: rsem: Remove trailing #T from snippet. 
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
 2021-12-04 15:25:26 +01:00
Ricardo Wurmus
cfaf37d10b
gnu: prodigal: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:13:11 +01:00
Ricardo Wurmus
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
 2021-12-04 15:11:28 +01:00
Ricardo Wurmus
e128839a94
gnu: prank: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:11:04 +01:00
Ricardo Wurmus
114eb987cb
gnu: mash: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
 2021-12-04 00:32:01 +01:00
Ricardo Wurmus
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs. 
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
 2021-12-04 00:31:20 +01:00
Ricardo Wurmus
a6b6084649
gnu: mash: Simplify snippet. 
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
 2021-12-04 00:30:44 +01:00
Ricardo Wurmus
31409a4af7
gnu: mafft: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 00:22:27 +01:00
Ricardo Wurmus
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
 2021-12-04 00:21:27 +01:00
Ricardo Wurmus
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
 2021-12-04 00:19:08 +01:00
Ricardo Wurmus
7c2ee27360
gnu: fastp: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
 2021-12-04 00:16:10 +01:00
Ricardo Wurmus
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
 2021-12-04 00:06:43 +01:00
Ricardo Wurmus
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
 2021-12-04 00:03:54 +01:00
Ricardo Wurmus
62e0641892
gnu: fxtract: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
 2021-12-04 00:02:20 +01:00
Ricardo Wurmus
4f03151ca4
gnu: delly: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-04 00:00:26 +01:00
Ricardo Wurmus
3601fcbf65
gnu: libbigwig: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:57:24 +01:00
Ricardo Wurmus
fd607a9efa
gnu: cd-hit: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
 2021-12-03 23:56:11 +01:00
Ricardo Wurmus
c40852a227
gnu: bowtie1: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-03 23:54:10 +01:00
Ricardo Wurmus
a47a90b900
gnu: bowtie: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:52:43 +01:00
Ricardo Wurmus
f5c38ee45f
gnu: bless: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp.  Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
 2021-12-03 23:51:16 +01:00
Ricardo Wurmus
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases. 
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
 2021-12-03 23:48:46 +01:00
Ricardo Wurmus
0e09065460
gnu: bedtools: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
 2021-12-03 23:36:18 +01:00
Ricardo Wurmus
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
 2021-12-03 23:26:48 +01:00
Ricardo Wurmus
6d4f260166
gnu: bamutils: Update to 1.0.14. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
 2021-12-03 13:56:02 +01:00
Ricardo Wurmus
673cc29908
gnu: bamutils: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
361e0d9f27
gnu: bamm: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
 2021-12-03 13:56:01 +01:00