CVS log for pkgsrc/biology/canu/Makefile

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Default branch: MAIN

Revision 1.22 / (download) - annotate - [select for diffs], Thu Jun 1 03:33:03 2023 UTC (9 days, 2 hours ago) by wiz
Branch: MAIN
CVS Tags: HEAD
Changes since 1.21: +3 -3 lines
Diff to previous 1.21 (colored)

canu: use github framework variables

Revision 1.21 / (download) - annotate - [select for diffs], Sat May 20 14:42:11 2023 UTC (2 weeks, 6 days ago) by bacon
Branch: MAIN
Changes since 1.20: +8 -4 lines
Diff to previous 1.20 (colored)

biology/canu: Fix build on Darwin aarch64

Replace SIMDE with upstream source hacks from FreeBSD port
Should also work on powerpc, but untested
No changes to existing binaries

Revision 1.20 / (download) - annotate - [select for diffs], Sat May 20 11:27:27 2023 UTC (2 weeks, 6 days ago) by bacon
Branch: MAIN
Changes since 1.19: +10 -12 lines
Diff to previous 1.19 (colored)

biology/canu: Hacks to support Darwin x86

OpenMP support needs improvement
Darwin aarch64 still blocked by glib2 build issues
No changes to binaries on other platforms

Revision 1.19 / (download) - annotate - [select for diffs], Thu May 18 18:17:32 2023 UTC (3 weeks, 1 day ago) by bacon
Branch: MAIN
Changes since 1.18: +21 -16 lines
Diff to previous 1.18 (colored)

biology/canu: Update to 2.2

Numerous new features, enhancements, and bug fixes since 1.8
Enabled support for aarch64
May work on other 64-bit platforms, but untested

Changes: https://github.com/marbl/canu/releases

Revision 1.18 / (download) - annotate - [select for diffs], Sun Apr 23 14:26:11 2023 UTC (6 weeks, 5 days ago) by adam
Branch: MAIN
Changes since 1.17: +2 -2 lines
Diff to previous 1.17 (colored)

revbump for boost

Revision 1.17 / (download) - annotate - [select for diffs], Sun Jan 22 16:28:18 2023 UTC (4 months, 2 weeks ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2023Q1-base, pkgsrc-2023Q1
Changes since 1.16: +2 -2 lines
Diff to previous 1.16 (colored)

*: Recursive revbump from Boost 1.81.0

Revision 1.16 / (download) - annotate - [select for diffs], Tue Jun 28 11:31:00 2022 UTC (11 months, 1 week ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3
Changes since 1.15: +2 -2 lines
Diff to previous 1.15 (colored)

*: recursive bump for perl 5.36

Revision 1.15 / (download) - annotate - [select for diffs], Mon Jan 10 01:46:22 2022 UTC (16 months, 4 weeks ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

*: Recursive revbump from boost 1.78.0

Revision 1.14 / (download) - annotate - [select for diffs], Wed Sep 29 19:00:20 2021 UTC (20 months, 1 week ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.13: +2 -2 lines
Diff to previous 1.13 (colored)

revbump for boost-libs

Revision 1.13 / (download) - annotate - [select for diffs], Mon May 24 19:49:10 2021 UTC (2 years ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2
Changes since 1.12: +2 -2 lines
Diff to previous 1.12 (colored)

*: recursive bump for perl 5.34

Revision 1.12 / (download) - annotate - [select for diffs], Wed Apr 21 13:24:23 2021 UTC (2 years, 1 month ago) by adam
Branch: MAIN
Changes since 1.11: +2 -2 lines
Diff to previous 1.11 (colored)

revbump for boost-libs

Revision 1.11 / (download) - annotate - [select for diffs], Fri Jan 1 08:24:34 2021 UTC (2 years, 5 months ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1
Changes since 1.10: +2 -2 lines
Diff to previous 1.10 (colored)

*: Recursive revbump from boost-1.75.0

Revision 1.10 / (download) - annotate - [select for diffs], Mon Aug 31 18:06:38 2020 UTC (2 years, 9 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q4-base, pkgsrc-2020Q4, pkgsrc-2020Q3-base, pkgsrc-2020Q3
Changes since 1.9: +2 -2 lines
Diff to previous 1.9 (colored)

*: bump PKGREVISION for perl-5.32.

Revision 1.9 / (download) - annotate - [select for diffs], Sat May 16 19:40:59 2020 UTC (3 years ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base, pkgsrc-2020Q2
Changes since 1.8: +7 -17 lines
Diff to previous 1.8 (colored)

biology/canu: fix SUBST blocks to actually find the Java code

Revision 1.8 / (download) - annotate - [select for diffs], Thu May 14 18:30:05 2020 UTC (3 years ago) by rillig
Branch: MAIN
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored)

biology/canu: don't try to chmod system binaries

/usr/bin/chmod -R g-w /home/pbulk/build/biology/canu/work
chmod: WARNING: can't change /home/pbulk/build/biology/canu/work/.gcc/bin/cc
chmod: WARNING: can't change /home/pbulk/build/biology/canu/work/.gcc/bin/g++

Just good that serious pkgsrc builds are run as an unprivileged user,
with no chance of bricking the whole operating system.

Revision 1.7 / (download) - annotate - [select for diffs], Wed May 6 14:04:19 2020 UTC (3 years, 1 month ago) by adam
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 (colored)

revbump after boost update

Revision 1.6 / (download) - annotate - [select for diffs], Sun Jan 12 20:20:04 2020 UTC (3 years, 4 months ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2020Q1-base, pkgsrc-2020Q1
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 (colored)

*: Recursive revbump from devel/boost-libs

Revision 1.5 / (download) - annotate - [select for diffs], Thu Aug 22 12:22:51 2019 UTC (3 years, 9 months ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.4: +2 -2 lines
Diff to previous 1.4 (colored)

Recursive revbump from boost-1.71.0

Revision 1.4 / (download) - annotate - [select for diffs], Sun Aug 11 13:17:59 2019 UTC (3 years, 9 months ago) by wiz
Branch: MAIN
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored)

Bump PKGREVISIONs for perl 5.30.0

Revision 1.3 / (download) - annotate - [select for diffs], Mon Jul 1 04:07:57 2019 UTC (3 years, 11 months ago) by ryoon
Branch: MAIN
Changes since 1.2: +2 -1 lines
Diff to previous 1.2 (colored)

Recursive revbump from boost-1.70.0

Revision 1.2 / (download) - annotate - [select for diffs], Mon Jun 24 10:59:41 2019 UTC (3 years, 11 months ago) by nia
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

More http -> https.

Reviewed by hand.

Revision 1.1 / (download) - annotate - [select for diffs], Mon Jan 7 02:33:17 2019 UTC (4 years, 5 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2019Q1-base, pkgsrc-2019Q1

biology/canu: import canu-1.8

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

    Detect overlaps in high-noise sequences using MHAP

    Generate corrected sequence consensus

    Trim corrected sequences

    Assemble trimmed corrected sequences

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