Port details on branch 2022Q3 |
- 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TopHat has been Superseded by HISAT2 and is no longer maintained upstream.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
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
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- 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:
-
- gmake : devel/gmake
- python2.7 : lang/python27
- Runtime dependencies:
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- 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:
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