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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
27 stars 7 forks source link

examples & where to store BioNano scripts/tools #3

Closed liuqianhn closed 7 years ago

liuqianhn commented 7 years ago

Hi, may I know where to store BioNano scripts/tools so that runBNG can find them? Do you have examples how to runBNG? Thanks.

yyx8671 commented 7 years ago

@liuqianhn For the settings and how to run 'runBNG', you may refer https://github.com/AppliedBioinformatics/runBNG/blob/master/Manual.md. The test data is available at https://github.com/AppliedBioinformatics/runBNG/tree/master/Examples. For the BioNano scripts and tools, you can download them to any directory on your Linux cluster, but give them a readable and executable permission.

liuqianhn commented 7 years ago

Hi Andy, thank you very much.

May I know how can I run runBNG with glibc 2.14? I cannot install higher version of glibc in my system.

yyx8671 commented 7 years ago

@liuqianhn Glibc is required by RefAligner/Assembler. I have tested the old version, such as 'glibc 2.11.3' on SUSE Linux and it works, but for other Linux system, such as CentOS, it may not work.

The easy way to install 'glibc' is to use Linuxbrew, which I have indicated in the Manual. You may refer to it.

If you don't want to install Linuxbrew, you may disable the code in 'runBNG' from line 92 to 108 by adding "#" to the very beginning of each line, and test whether the whole runBNG pipeline works properly on your system.

liuqianhn commented 7 years ago

Hi Andy, Thank you very much for your help. I used CentOS. I tried to used older version of RefAligner/Assembler. It could work with glibc 2.14. I will try your suggestions also. Thanks.