| Port details |
- tophat Fast splice junction mapper for RNA-Seq reads
- 2.1.1_1 biology
 =0      2.1.1_1Version of this port present on the latest quarterly branch.  DEPRECATED: Uses deprecated version of python
 This port expired on: 2020-09-15
- Maintainer: jwb@FreeBSD.org
- 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TopHat has been Superseded by HISAT2 and is no longer maintained upstream.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
 cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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
No package information for this port in our database- Sometimes this happens. Not all ports have packages.
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake : devel/gmake
- python2.7 : lang/python27
- Runtime dependencies:
-
- bowtie2 : biology/bowtie2
- python2.7 : lang/python27
- Library dependencies:
-
- 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:
|
Number of commits found: 4
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.1.1_1
19 Sep 2020 13:01:00
  |
rene |
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  ) |
2.1.1_1
08 Mar 2020 17:01:47
|
antoine |
Deprecate some ports using deprecated version of python
With hat: portmgr |
2.1.1_1
11 Dec 2019 17:53:49
|
jbeich |
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
|
jwb |
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
|
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