Difference between revisions of "Known Issues"
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===Some services under Sequence Alignment are not working=== | ===Some services under Sequence Alignment are not working=== | ||
Besides BLAST, there are three other tabs under Sequence Alignment: BLAT, HMM, and Other Algorithms. The BLAT tab should not have been included in the geWorkbench 1.0.5 release, as this is unsupported code. (It is an interface to a copy of BLAT you would install separately on your own desktop machine). HMM and the algorithms under Other are not functional because the hardware accelerator that provided them, a GeneMatcher2, is no longer in service. These tabs will likely be removed in the next release. | Besides BLAST, there are three other tabs under Sequence Alignment: BLAT, HMM, and Other Algorithms. The BLAT tab should not have been included in the geWorkbench 1.0.5 release, as this is unsupported code. (It is an interface to a copy of BLAT you would install separately on your own desktop machine). HMM and the algorithms under Other are not functional because the hardware accelerator that provided them, a GeneMatcher2, is no longer in service. These tabs will likely be removed in the next release. | ||
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Revision as of 15:20, 1 May 2007
Some services under Sequence Alignment are not working
Besides BLAST, there are three other tabs under Sequence Alignment: BLAT, HMM, and Other Algorithms. The BLAT tab should not have been included in the geWorkbench 1.0.5 release, as this is unsupported code. (It is an interface to a copy of BLAT you would install separately on your own desktop machine). HMM and the algorithms under Other are not functional because the hardware accelerator that provided them, a GeneMatcher2, is no longer in service. These tabs will likely be removed in the next release.
Some examples of errors seen are:
/usr/lib/jvm/jre-1.5.0-sun/bin/java: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory /usr/lib/jvm/jre-1.5.0-sun/bin/java: error while loading shared libraries: libpthread.so.0: cannot open shared object file: No such file or directory
This is a known problem with the version of InstallAnywhere used to create the distribution packages for geWorkbench. The problem will be fixed in coming geWorkbench distributions. However, in general, the installer file can be patched as follows:
Run a command like the following to comment out the line giving problems:
perl -pi -e 's/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/'geWorkbench_v1.0.5_Linux_installer.bin
and then run
sh ./geWorkbench_v1.0.5_Linux_installer.bin
