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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greyltc commented on 2015-03-14 20:09 (UTC)

Unfortunately I'm not having luck with your update. Here's the relevant output: http://pastebin.com/kFvgKDWH

wookietreiber commented on 2015-03-11 11:36 (UTC)

Please try this update.

wookietreiber commented on 2015-03-11 10:55 (UTC)

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 (UTC)

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 (UTC)

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

wookietreiber commented on 2014-11-12 20:58 (UTC)

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 (UTC)

-- 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 (UTC)

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 (UTC)

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 (UTC)

I got it to compile with clang and -j1.

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