[med-svn] [Git][med-team/canu][master] 14 commits: New upstream version 1.7+dfsg

[Afif Elghraoui]

Afif Elghraoui pushed to branch master at Debian Med / canu


Commits:
243aa28b by Afif Elghraoui at 2018-03-10T17:09:47-05:00
New upstream version 1.7+dfsg
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72ffbdd9 by Afif Elghraoui at 2018-03-10T17:09:51-05:00
Merge tag 'upstream/1.7+dfsg'

Upstream version 1.7+dfsg

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df269544 by Afif Elghraoui at 2018-03-10T18:51:20-05:00
Update handling of MHAP copy

The jar file is bundled rather than its source code.
The patches to exclude the build directory aren't needed,
but Files-Excluded needed to be changed.

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aba64962 by Afif Elghraoui at 2018-03-10T18:52:20-05:00
Refresh patches

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ceb7a203 by Afif Elghraoui at 2018-03-10T18:52:20-05:00
use a wrapper script and leave /usr/lib/canu/ as undisturbed as possible

Rather than patching paths, let the canu main program live where
it expects to be, just using a wrapper script in /usr/bin.

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6f15624a by Afif Elghraoui at 2018-03-10T18:53:46-05:00
New upstream version 1.7+dfsg
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24d6be52 by Afif Elghraoui at 2018-03-10T18:53:50-05:00
Merge tag 'upstream/1.7+dfsg'

Upstream version 1.7+dfsg

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5419d316 by Afif Elghraoui at 2018-03-10T19:08:53-05:00
Remove build system dependency on bundled MHAP

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0ce0b35d by Afif Elghraoui at 2018-03-10T19:25:44-05:00
fix typo in patch

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2454ffa4 by Afif Elghraoui at 2018-03-10T19:48:01-05:00
fix path to mhap jar

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d8b271be by Afif Elghraoui at 2018-03-10T19:48:21-05:00
move gnuplot to Depends

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ae4c2a99 by Afif Elghraoui at 2018-03-10T20:16:24-05:00
Bump mhap minimum version

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b673b3d8 by Afif Elghraoui at 2018-03-10T20:17:39-05:00
Bump Standards-Version to 4.1.3

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4eafc31f by Afif Elghraoui at 2018-03-10T23:45:30-05:00
Update changelog (need update to mhap package)

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30 changed files:

- README.md
- addCopyrights-BuildData.pl
- addCopyrights.dat
- addCopyrights.pl
- + debian/bin/canu
- debian/changelog
- debian/control
- debian/copyright
- debian/install
- − debian/links
- − debian/patches/external-deps.patch
- + debian/patches/external-mhap.patch
- debian/patches/gcc-7_format-security.patch
- − debian/patches/relative-paths.patch
- debian/patches/series
- debian/patches/use-debian-mhap-at-runtime.patch
- debian/rules
- documentation/reST-markup-hints
- documentation/source/conf.py
- documentation/source/faq.rst
- documentation/source/parameter-reference.rst
- documentation/source/quick-start.rst
- documentation/source/tutorial.rst
- src/AS_UTL/AS_UTL_alloc.H
- src/AS_UTL/AS_UTL_fasta.C
- src/AS_UTL/AS_UTL_fasta.H
- src/AS_UTL/AS_UTL_fileIO.C
- src/AS_UTL/AS_UTL_fileIO.H
- src/AS_UTL/AS_UTL_reverseComplement.C
- src/AS_UTL/AS_UTL_reverseComplement.H


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/canu/compare/5bffe33302bbe0f1210c01a75d6b0ca04b026ffa...4eafc31fe7e77b532289eb68cff4b3e81970b033

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View it on GitLab: https://salsa.debian.org/med-team/canu/compare/5bffe33302bbe0f1210c01a75d6b0ca04b026ffa...4eafc31fe7e77b532289eb68cff4b3e81970b033
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