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Why was the website so slow for so long?

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.

non port: biology/tophat/Makefile

Number of commits found XX: 3

Sun, 8 Mar 2020
[ 17:01 antoine ] Original commit   Revision:528058
528058 audio/abraca/Makefile
528058 audio/ardour5/Makefile
528058 audio/cplay/Makefile
528058 audio/cpp-xmms2/Makefile
528058 audio/exaile/Makefile
528058 audio/p5-xmms2/Makefile
528058 benchmarks/glmark2/Makefile
528058 biology/haplohseq/Makefile
528058 biology/tophat/Makefile
528058 cad/lepton-eda/Makefile

(Only the first 10 of 187 ports in this commit are shown above. View all ports for this commit)
Deprecate some ports using deprecated version of python

With hat:	portmgr
Wed, 11 Dec 2019
[ 17:53 jbeich ] Original commit   Revision:519824
519824 archivers/innoextract/Makefile
519824 archivers/tardy/Makefile
519824 astro/libkgeomap/Makefile
519824 astro/libosmium/Makefile
519824 audio/ardour/Makefile
519824 audio/ardour5/Makefile
519824 audio/clementine-player/Makefile
519824 audio/cpp-xmms2/Makefile
519824 audio/csound/Makefile
519824 audio/faust-lv2/Makefile

(Only the first 10 of 417 ports in this commit are shown above. View all ports for this commit)
devel/boost-*: update to 1.72.0

PR:		241449
Exp-run by:	antoine
Differential Revision:
Fri, 27 Sep 2019
[ 00:49 jwb ] Original commit   Revision:512997
512997 biology/Makefile
512997 biology/tophat
512997 biology/tophat/Makefile
512997 biology/tophat/distinfo
512997 biology/tophat/files
512997 biology/tophat/files/patch-configure
512997 biology/tophat/files/patch-src-samtools-0.1.18-Makefile
512997 biology/tophat/files/
512997 biology/tophat/files/tophat-test
512997 biology/tophat/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
biology/tophat: Fast splice junction mapper for RNA-Seq reads

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.


TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.

Number of commits found XX: 3

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