geWorkbench

geWorkbench 1.0.5

NCBI BLAST results cannot be parsed into geWorkbench 1.0.5

Due to a recent change in the format of the files returned by the NCBI BLAST service, these results cannot be parsed into geWorkbench 1.0.5. The problem has been fixed in the development version of geWorkbench. This version can be compiled from source available at the geWorkbench GForge site.

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.

When using certain versions of Linux, you may receive errors indicating problems with loading shared libraries.

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(s) giving problems, where install.bin represents the install file (which will have a different name in the actual release):

(New way) mv install.bin install.bak

cat install.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > install.bin
sh install.bin

(Old way)

perl -pi -e 's/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/'install.bin

and then run

sh ./install.bin