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genome center home > arachne > FAQ
 

Arachne: A Whole Genome Assembly Software Package

 

Frequently Asked Questions

1. Can I install Arachne on a Linux/Intel platform?

Yes. This is possible, but unsupported. To the best of our knowledge, it works fine: we compiled and ran Arachne on a standard Linux/Intel box (Debian 3.0 "Woody"), and the binaries are available on-line. However, we have not thoroughly tested it, and at this time we are too busy to support more than one platform. What we can do is maintain a list of people who have successfully installed on the Linux/Intel platform and are willing to share their expertise:

Intel Linux binaries are available at: ftp://ftp.broad.mit.edu/pub/wga/unsupported/Arachne_v2.0.1_Linux/.

2. Can I install Arachne on some other platform?

To the best of our knowledge, no one has tried. If the platform does not support gcc 2.95.2 or has a big endian architecture, significant reengineering may be required.

3. I get the following error when I run Assemble: 

Welcome to Arachne!
Copyright (c) 2000, 2001 Whitehead Institute for Biomedical Research.
See LICENSE.txt for details.

Mon Jun 24 16:04:53 2002.  Segmentation violation.

Generating a backtrace...

Dump of stack:

2. String::String(char const *), in String.cc:218
3. String::String(char const *), in String.cc:218
4. main, in Assemble.cc:416

What can I do?

You've found a bug that only appears if your environment does not contain the variable LD_LIBRARY_PATH. To fix it, set that variable to some value, such as "/usr/lib".




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