notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

Two new features

Two new features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
Port details
tophat Fast splice junction mapper for RNA-Seq reads
2.1.1_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 View this port on Repology. 2.1.1_1Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Uses deprecated version of python
Expiration Date EXPIRATION DATE: 2020-09-15
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-09-27 00:49:58
Last Update: 2020-03-08 17:01:47
SVN Revision: 528058
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_1/catalog.mk
  2. /usr/local/share/licenses/tophat-2.1.1_1/LICENSE
  3. /usr/local/share/licenses/tophat-2.1.1_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:
  • ${PYTHON_PKGNAMEPREFIX}>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:
Packages: (move your mouse over the cells for more information)
tophat
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.1.1_12.1.1_1
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.1.1_12.1.1_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642.1.1_1-
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
 

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: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
08 Mar 2020 17:01:47
Original commit files touched by this commit  2.1.1_1
Revision:528058
antoine search for other commits by this committer
Deprecate some ports using deprecated version of python

With hat:	portmgr
11 Dec 2019 17:53:49
Original commit files touched by this commit  2.1.1_1
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
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: 3

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
apache24*Aug 08
gitlab-ceAug 06
goAug 06
sqlite3*Aug 06
typo3-10Aug 04
typo3-9Aug 04
libX11Aug 01
xephyrAug 01
xorg-dmxAug 01
xorg-nestserverAug 01
xorg-serverAug 01
xorg-vfbserverAug 01
xwaylandAug 01
python38Jul 31
arkJul 30

14 vulnerabilities affecting 93 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2020-08-09 09:02:56


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 40280
Broken 89
Deprecated 602
Ignore 325
Forbidden 5
Restricted 147
No CDROM 76
Vulnerable 20
Expired 3
Set to expire 572
Interactive 0
new 24 hours 3
new 48 hours7
new 7 days22
new fortnight60
new month137

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2020 Dan Langille. All rights reserved.