Package Details: tophat 2.1.1-2

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: greyltc
Last Packager: wookietreiber
Votes: 10
Popularity: 0.000000
First Submitted: 2012-01-20 00:50
Last Updated: 2016-06-02 09:33

Latest Comments

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wookietreiber commented on 2015-03-11 11:36

Please try this update.

wookietreiber commented on 2015-03-11 10:55

I'm trying ATM to create a build that works without the included samtools and seqan dependencies.

greyltc commented on 2015-03-10 17:59

This seems to still be failing to build for me.
Does anyone have a patch? or are we all just waiting for upstream to fix this?

khughitt commented on 2014-11-13 11:40

Upstream issue: https://groups.google.com/forum/#!topic/tuxedo-tools-users/M7Z9zLuu8o4

wookietreiber commented on 2014-11-12 20:58

What I don't get is why they have -g -gdwarf-2 enabled ...

I toyed a bit around with the patches of debian but so far no joy.

khughitt commented on 2014-11-12 11:48

-- tophat 2.0.13 Configuration Results --
C++ compiler: clang++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3
Linker flags: -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro
BOOST libraries: -lboost_thread -lboost_system
GCC version: clang version 3.5.0 (tags/RELEASE_350/final)
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}

wookietreiber commented on 2014-11-11 15:11

Mine fails at target reads.o with gcc.

How does this look at your machine from configure output?

-- tophat 2.0.13 Configuration Results -- [160/920]
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -march=native -mfpmath=sse -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -DNDEBUG -pth
read -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3
Linker flags: -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro
BOOST libraries: -lboost_thread -lboost_system
GCC version: gcc (GCC) 4.9.2
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}

khughitt commented on 2014-11-08 17:17

Still getting errors on my end:

clang: error: linker command failed with exit code 1 (use -v to see invocation)
Makefile:1100: recipe for target 'prep_reads' failed
make[2]: *** [prep_reads] Error 1
make[2]: Leaving directory '/tmp/yaourt-tmp-xx/aur-tophat/src/tophat-2.0.13/src'
Makefile:243: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-xx/aur-tophat/src/tophat-2.0.13'
Makefile:181: recipe for target 'all' failed
make: *** [all] Error 2

wookietreiber commented on 2014-11-07 14:36

I got it to compile with clang and -j1.

khughitt commented on 2014-10-04 15:05

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