| Commit message (Collapse) | Author | Age | Files | Lines |
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Release 0.7.16 (30 July 2017)
-----------------------------
This release added a couple of minor features and incorporated multiple pull
requests, including:
* Added option -5, which is useful to some Hi-C pipelines.
* Fixed an error with samtools sorting (#129). Updated download link for
GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple
issues via a collected pull request #139 by @jmarshall. Avoid malformatted
SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).
This release is expected to give the same alignment as 0.7.15, except the added
mate-cigar tag.
(0.7.16: 30 July 2017, r1180)
https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Sorry for noise.
Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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upstream
Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Package-Manager: Portage-2.3.6, Repoman-2.3.3
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Cannot proceed unless htslib-1.5 can be properly installed along existing
htslib-1.3.1 installation.
Package-Manager: Portage-2.3.6, Repoman-2.3.2
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This should be kept unmasked as it uses bundled static lib of htslib-1.5
so practically avoid dependency on sci-libs/htslib-1.5.
Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Keeping KEYWORDS empty because it conflicts with htslib-1.3.1 as of now
unless jlec/soap proceed in some proper way.
Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Package-Manager: Portage-2.3.5, Repoman-2.3.2
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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We'll have to migrate to EAPI 6 at some point
Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Package-Manager: portage-2.3.6
Closes: https://github.com/gentoo/sci/pull/795
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Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Patch from upstream is required to build the shared library:
https://sourceforge.net/p/math-atlas/bugs/260/
Closes: https://github.com/gentoo/sci/pull/794
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Helps sorting out #794
Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Package-Manager: Portage-2.3.5, Repoman-2.3.1
Closes: https://github.com/gentoo/sci/pull/792
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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Package-Manager: Portage-2.3.6, Repoman-2.3.2
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1) acml is linked with opencl support:
libclFFT.so.2.3.1, libclBLAS.so.2.3.0, libacml_bridge.so.1.1.28:
libOpenCL.so.1 => not found
2) update to EAPI 6.
Package-Manager: Portage-2.3.6, Repoman-2.3.2
Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
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Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Closes: https://github.com/gentoo/sci/issues/709
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sci-libs/lapack-reference: configure BLAS_LIBRARIES implicitly
cmake option USE_OPTIMIZED_BLAS uses pkg-config to figure out
BLAS_LIBRARIES in Gentoo FindBLAS cmake patch.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
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same rational as commit e6181c66eac for lapack-reference.
alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare
quotes confuses cmake parser. Escaping the quotes is tedious,
but solves the problem.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
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alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare
quotes confuses cmake parser. Escaping the quotes is tedious,
but solves the problem.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
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Update the use flags.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Package-Manager: Portage-2.3.3, Repoman-2.3.1
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Required petsc versions were removed from the overlay.
Package-Manager: Portage-2.3.5, Repoman-2.3.1
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s/gentoo-sci/gentoo/g
Signed-off-by: Marius Brehler <marbre@linux.sungazer.de>
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