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Old 08-11-2010, 05:47 AM   #1
Telor
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Default Cufflinks executables not working

Hi,

I hoping someone might be able to help me get cufflinks working on our system. I have cufflinks v0.8.1 working (using the provided executables) but every version released since then all three executables (64bit) have just crashed with a floating point exception when I tried to call them.

Our system's kernel is Linux 2.6.16.60-0.21-smp x86_64.

To try to get around this, I've tried to build a version on our system using the provided sources. I've installed the boost libraries and during the configuration everything goes fine until it gets to the check for bamlib, which it says is not installed. Thats no problem, except I can't find it anywhere to install, the error refers me to a site: http://randspringer.de/bam which doesn;t exist anymore.

After hours searching I hadto give up, but the version of cufflinks I have running is crashing on a large dataset I'm trying to run, so its becoming urgent that I update.

Can anyone point me in the right direction for either getting the executables working on my system (I'm not sure that's possible), or point me to where I can find these Bam libraries so I can build the executables myself.

Any help would be greatly appreciated. I attach the "./configure" output for reference, maybe its just that I'm doing something stupid.

Thanks,

Chris.


cufflinks-0.8.4> ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for boostlib >= 1.38.0... yes
checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.
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Old 08-11-2010, 11:57 PM   #2
sanwen
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I face this problem too. Waiting for answer.
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Old 10-04-2010, 08:52 AM   #3
scozza
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I've hit this too. I am trying it with the flag "--without-bam". Will update if I get it to compile and run.

Last edited by scozza; 10-04-2010 at 08:54 AM.
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Old 10-04-2010, 09:03 AM   #4
scozza
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Nope not the solution. I then thought perhaps it was the C++ API BamTools but that doesn't seem right either.
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Old 10-04-2010, 09:06 AM   #5
adarob
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The instructions on this page should do the trick:

http://cufflinks.cbcb.umd.edu/tutorial.html
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Old 10-04-2010, 09:11 AM   #6
scozza
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Thanks. I'm relying on Google too much these days!
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Old 10-04-2010, 09:25 AM   #7
Telor
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I Finally got this to compile using the instructions released with the new version of cufflinks (linked above). But even though I get an executable that starts properly, I now get a core dump when I run it. In case this is due to the changes in the SAM headers required for this version of cufflinks, I've installed the new version of tophat ro re-run my alignments etc..

However....

Now Tophat is not working properly, it is exiting with an error that is described in this thread:
http://seqanswers.com/forums/showthread.php?t=7118

This is getting very frustrating
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