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Things are slow!

Some of the pages ont the website are slow. I know diskio is way up. I don't know what it is but it's been going on for about three weeks. It might have been a change to the zpool recordsize on the PostgreSQL database dataset.

One way to know: copy the dataset to another dataset with the original recordsize and use that. I hope can get to that later this week.

I have not tackled the issue yet because I've been concentrating on the BSDCan and PGCon calls for papers.

Port details
tophat Fast splice junction mapper for RNA-Seq reads
2.1.1 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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-09-27 00:49:58
Last Update: 2019-09-27 01:49:49
SVN Revision: 512997
Also Listed In: python
License: BSL
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (32 items)
  1. /usr/local/share/licenses/tophat-2.1.1/catalog.mk
  2. /usr/local/share/licenses/tophat-2.1.1/LICENSE
  3. /usr/local/share/licenses/tophat-2.1.1/BSL
  4. bin/bam2fastx
  5. bin/bam_merge
  6. bin/bed_to_juncs
  7. bin/contig_to_chr_coords
  8. bin/fix_map_ordering
  9. bin/gtf_juncs
  10. bin/gtf_to_fasta
  11. bin/intervaltree/__init__.py
  12. bin/intervaltree/interval.py
  13. bin/intervaltree/intervaltree.py
  14. bin/intervaltree/node.py
  15. bin/juncs_db
  16. bin/long_spanning_reads
  17. bin/map2gtf
  18. bin/prep_reads
  19. bin/sam_juncs
  20. bin/samtools_0.1.18
  21. bin/segment_juncs
  22. bin/sortedcontainers/__init__.py
  23. bin/sortedcontainers/sorteddict.py
  24. bin/sortedcontainers/sortedlist.py
  25. bin/sortedcontainers/sortedlistwithkey.py
  26. bin/sortedcontainers/sortedset.py
  27. bin/sra_to_solid
  28. bin/tophat
  29. bin/tophat-fusion-post
  30. bin/tophat-test
  31. bin/tophat2
  32. bin/tophat_reports
Collapse this list.
Dependency lines:
  • tophat>0:biology/tophat
To install the port: cd /usr/ports/biology/tophat/ && make install clean
To add the package: pkg install tophat
PKGNAME: tophat
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. gmake : devel/gmake
  2. python2.7 : lang/python27
Runtime dependencies:
  1. bowtie2 : biology/bowtie2
  2. python2.7 : lang/python27
Library dependencies:
  1. libboost_iostreams.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. http://ccb.jhu.edu/software/tophat/downloads/

Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
27 Sep 2019 00:49:49
Original commit files touched by this commit  2.1.1
Revision:512997
jwb search for other commits by this committer
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.

Note:

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: 1

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