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Port details
tophat Fast splice junction mapper for RNA-Seq reads
2.1.1_1 biology Deleted 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. pkg-fallout 2.1.1_1Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Uses deprecated version of python
Expired This port expired on: 2020-09-15
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-09-27 00:49:58
Last Update: 2020-09-19 13:01:00
SVN Revision: 548980
Also Listed In: python
License: BSL
WWW:
http://ccb.jhu.edu/software/tophat/index.shtml
Description:
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 Note: TopHat has been Superseded by HISAT2 and is no longer maintained upstream.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. WWW: http://ccb.jhu.edu/software/tophat/index.shtml
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (32 items)
Collapse this list.
  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
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Dependency lines:
  • tophat>0:biology/tophat
No installation instructions:
This port has been deleted.
PKGNAME: tophat
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1522620646 SHA256 (tophat-2.1.1.tar.gz) = 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SIZE (tophat-2.1.1.tar.gz) = 2259554

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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:
No options to configure
Options name:
N/A
USES:
gmake python:2.7 shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
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  1. http://ccb.jhu.edu/software/tophat/downloads/
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Number of commits found: 4

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.1.1_1
19 Sep 2020 13:01:00
Revision:548980Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:

2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.1.1_1
08 Mar 2020 17:01:47
Revision:528058Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate some ports using deprecated version of python

With hat:	portmgr
2.1.1_1
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
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
2.1.1
27 Sep 2019 00:49:49
Revision:512997Original commit files touched by this commit
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: 4