bamliquidator: Installation issues about pipeline HOT 6 CLOSED

Hi venuthatikonda, very sorry for the delayed response.

bamliquidator expects samtools version 0.1.19, e.g. as installed by the Ubuntu 14.04 package libbam-dev. Your build is failing because g++ is finding a newer version of samtools.

Please try the following from the pipeline/bamliquidator_internal directory:

make clean
CPLUS_INCLUDE_PATH=/usr/include make

If that doesn't help, please provide the output of cat /etc/issue and I'll follow up further. Also, you may consider using the pre-compiled binaries by following these instructions instead: https://github.com/BradnerLab/pipeline/wiki/motif_liquidator#1-download (just extract the contents with those binaries into your bamliquidator_internal directory).

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Hi John,

Thanks for the suggestions.

I downloaded the pre-compiled binaries Redhat/cent OS version. ./cpp_test is showing PASSED but when I actually run the ./bamliquidator it is giving the following error

./bamliquidator: error while loading shared libraries: libbam.so.1: cannot open shared object file: No such file or directory

Is it still because latest samtools version? Should I install the 0.1.19?

I'm using openSUSE Leap 42.1 - Kernel.

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Is there any chance that this will be updated to the latest samtools (1.6 atm)? I am installing these by hand, so it's no issue, but that is a very old samtools

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motif liquidator looks ok, but bamliquidator is explicitly listed as a dependency for Rose2 and coltron :/

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@datakid sorry, I don't have any plans to upgrade to latest samtools, but patches are welcome

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Closing because this issue is very old and I hope I addressed the original questions. If there are additional questions, please open a new issue.

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