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The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

Port details
cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
2.2.1.83_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.2.1.83Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-25 22:28:39
Last Update: 2019-12-11 17:53:49
SVN Revision: 519824
License: BSL
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (12 items)
  1. bin/compress_gtf
  2. bin/cuffcompare
  3. bin/cuffdiff
  4. bin/cufflinks
  5. bin/cuffmerge
  6. bin/cuffnorm
  7. bin/cuffquant
  8. bin/gffread
  9. bin/gtf_to_sam
  10. /usr/local/share/licenses/cufflinks-2.2.1.83_2/catalog.mk
  11. /usr/local/share/licenses/cufflinks-2.2.1.83_2/LICENSE
  12. /usr/local/share/licenses/cufflinks-2.2.1.83_2/BSL
Collapse this list.
Dependency lines:
  • cufflinks>0:biology/cufflinks
To install the port: cd /usr/ports/biology/cufflinks/ && make install clean
To add the package: pkg install cufflinks
PKGNAME: cufflinks
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. eigen3.pc : math/eigen3
  2. gmake : devel/gmake
  3. python3.6 : lang/python36
  4. autoconf>=2.69 : devel/autoconf
  5. automake>=1.16.1 : devel/automake
Runtime dependencies:
  1. python3.6 : lang/python36
Library dependencies:
  1. libboost_system.so : devel/boost-libs
  2. libhts.so : biology/htslib
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/cole-trapnell-lab/cufflinks/tar.gz/v2.2.1-83-gb4fa050?dummy=/

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Dec 2019 17:53:49
Original commit files touched by this commit  2.2.1.83_2
Revision:519824
jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
19 Aug 2019 15:35:28
Original commit files touched by this commit  2.2.1.83_1
Revision:509290
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
29 May 2019 07:02:28
Original commit files touched by this commit  2.2.1.83
Revision:502929
yuri search for other commits by this committer
biology/cufflinks: Fix build on i386 by removing the hard-coded -m64

Reported by:	fallout
25 May 2019 22:28:12
Original commit files touched by this commit  2.2.1.83
Revision:502661
yuri search for other commits by this committer
New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their
abundance, etc

Number of commits found: 4

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