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 2015-05-27 09:01

I wasn't aware they needed it. I removed the need for it in configure.ac, see https://github.com/wookietreiber/PKGBUILDs/commit/21dafd4cc4fd339b913dc730022f984c4493cb89

greyltc commented on 2015-05-26 19:26

Please add `subversion` to the makedepends or somehow patch out the call to svnversion stemming from `autoreconf -fi` in prepare()

wookietreiber commented on 2015-03-18 14:21

We still need to use clang, though. Tried reverting that, but no joy.

greyltc commented on 2015-03-18 14:20

That works. Thanks!

wookietreiber commented on 2015-03-18 14:04

2.0.13-3 includes the fix.

wookietreiber commented on 2015-03-18 13:55

Considering this is my linker command line:

clang++ -O3 -march=native -mfpmath=sse -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -L/
usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro -o prep_reads prep_reads.
o ../src/libtophat.a -lbam -lz

This sequence of flags is particularly weird:

-L/usr/lib -L./samtools-0.1.18 -Wl,... -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18

The -L flags are searched *in order*, i.e. by removing the -L/usr/lib flags we should be able to solve this issue.

wookietreiber commented on 2015-03-18 13:35

libbam.a is provided by samtools, as in https://github.com/samtools/samtools.

tophat release notes for 2.0.13:

> removed SAMtools as an external dependency in order to avoid incompatibility
> issues with recent and future changes of SAMtools and its code library (an
> older, stable SAMtools version is now packaged with TopHat)

good luck getting them to revert this ;)

as I have mentioned before, we need to figure out a way for the tophat build to ignore /usr/lib/libbam.a if samtools is installed in favor of the one included with tophat. I always thought linker -Lpath would do that ... apparently not.

greyltc commented on 2015-03-18 11:34

You were right! Removing samtools solves the issue.

Do you know what is the proper upstream project for libbam.a? If it's samtools, then I guess the proper solution is to submit a patch to tophat upstream to bring it up to make it compatible with the current libbam.a and then make samtools a build dependency for this package.

wookietreiber commented on 2015-03-16 10:23

I think, I get why your build fails, @greyltc:

The linker is trying to link against your locally installed libbam.a because it tries to lookup functions in /usr/lib/libbam.a instead of in the libbam.a provided with tophat.

Would you please try again by first removing your samtools (pacman -R samtools) and then building tophat?

The samtools version provided with tophat (0.1.18) is most likely incompatible with the one you have installed, which is why linking fails.

In case this works, all we need to figure out, I guess, is how to tell the tophat building process to ignore /usr/lib/libbam.a in favor of the one provided with tophat so users don't have to uninstall samtools if they want to build tophat.

greyltc commented on 2015-03-14 20:09

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