Package Details: tophat 2.1.2-3

Git Clone URL: https://aur.archlinux.org/tophat.git (read-only, click to copy)
Package Base: tophat
Description: fast splice junction mapper for RNA-Seq reads
Upstream URL: http://ccb.jhu.edu/software/tophat/index.shtml
Licenses: custom
Submitter: stratust
Maintainer: malacology (BioArchLinuxBot, sukanka)
Last Packager: BioArchLinuxBot
Votes: 10
Popularity: 0.000000
First Submitted: 2012-01-20 00:50 (UTC)
Last Updated: 2023-06-01 21:28 (UTC)

Latest Comments

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khughitt commented on 2014-10-04 15:05 (UTC)

Still no luck compiling. Going to orphan for now to allow someone with more time to try and tackle. If anyone is interested, you may want to start by checking out the debian version: https://packages.qa.debian.org/t/tophat.html

MikeDacre commented on 2014-07-21 22:54 (UTC)

Every version is currently not compiling, not just the latest version. I tried to fix the compilation problems, but no luck yet, I think it is an issue with the latest gcc. I have emailed the developers. In the meantime, I have created a binary version of this package: https://aur.archlinux.org/packages/tophat-bin/ Also, the URL for tophat has now changed to: http://ccb.jhu.edu/software/tophat/downloads/$pkgname-$pkgver.tar.gz

khughitt commented on 2014-07-04 13:37 (UTC)

Most recent version not compiling. Contacted authors about the issue, but let me know if you find a work-around in the meantime.

khughitt commented on 2012-11-02 13:22 (UTC)

working now. thanks!

stratust commented on 2012-11-01 16:18 (UTC)

Thanks khughitt to point out these issues. I updated the PKGBUILD to address them.

khughitt commented on 2012-11-01 15:21 (UTC)

Just tried installing using Yaourt and ran into a couple issues: 1) some of the launcher scripts in /usr/bin attempt to call binaries located in a yaourt temporary directory: # e.g. /usr/bin/tophat2 prefix="/tmp/yaourt-tmp-$USER/aur-tophat/pkg/usr" When attempting to run the result is: $ tophat2 /usr/bin/tophat2: line 15: /tmp/yaourt-tmp-(user)/aur-tophat/pkg/usr/bin/tophat: No such file or directory 2) /usr/bin/tophat calls /usr/bin/env python which for most systems will be Python 3; it works if the file is updated to call 'python2'. Thanks for putting this together!

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