Installing GotCloud on CentOS5

[Dan Mazur]

Some of the files distributed through the GotCloud github are pre-compiled binaries (in the gotcloud/bin folder before running make). These binaries appear to be compiled on a system with glibc version 2.7.

I am hoping to install GotCloud on an HPC cluster that runs CentOS 5 which does not support glibc version 2.7. So, I am not able to run these binaries.

I am able to compile the src directory, but when I run the tests, the snp test fails and the bottom of the umake.log file contains this error message:
/sb/software/tools/gotcloud/bin/bgzip: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /sb/software/tools/gotcloud/bin/bgzip)
make: *** [/sb/home/tfosrgm/gotcloud_test/testsnp/umaketest/vcfs/chr20/chr20.hardfiltered.vcf.gz.OK] Error 1

The align test passes successfully.

Is it possible to get the source code for the binaries in the gotcloud/bin directory? Or, if not, is it possible to get a copy of these files that were compiled on CentOS5 or another pre-glibc_2.7 OS?

Thank you for any help or advice you can offer.

Regards,

Dan

[Mary Kate Wing]

Dan,

Sorry about that.  I will add the source for those tools and make sure they are setup properly in a future release.

If I am looking at it correctly, it is just two programs: bgzip & tabix.

For now, here is a work-around.

bgzip is actually a part of samtools which we do distribute.  To build it:

cd gotcloud/src/samtools/

make bgzip

That should create gotcloud/src/samtools/bgzip

Setup a link in bin to point to that:

cd gotcloud/bin;

mv bgzip bgzip.old

ln -s ../src/samtools/bgzip .

That should take care of bgzip.

We do not already have tabix in the release.

You can download tabix from here:  https://github.com/samtools/tabix

There is a download zip button at the bottom of the list on the right side.

Or you can pull it using git.

Once you download (and uncompress), cd into that directory and type "make"

You can then copy or setup a link to that executable.

Let me know if this works for you, if you encounter any problems, or if you have any additional questions..

Mary Kate Wing

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[Dan Mazur]

Hello Mary Kate,

Thank you for your fast response. I recompiled the two binaries on my system and now both of the tests pass.

I should also mention that it was necessary for me to modify the file gotcloud/bin/umake.pl to replace every instance of make_path with mkpath. This is required when using any version of Perl earlier than 2.0.

Regards,

Dan

[Mary Kate Wing]

Great, glad that it works now.  Let me know if you need any help making use of gotCloud for your own data.

Thanks for letting me know what additional changes you needed to make.  I'll try to update future releases to fix that.