Debugging ZMap

Building ZMap

As follows (assumes you are using the C shell on a linux machine):


> setenv CVSROOT :ext:cvs.internal.sanger.ac.uk:/repos/cvs/zmap

> cd <directory where you want to checkout zmap>

> cvs checkout ZMap

> cd ZMap/src

> ./runbootstrap

> cd build/linux

> ../../runconfig

> make

> ./zmap --version

Debugging a ZMap problem reported by Havana

1: take a copy of their database

Ask the user to keep their lace session open while you take a copy of their database and ask them for their deskpro machine id (e.g. deskpro16113) and the path to their session (e.g. /var/tmp/laceXXXXXX).


> ssh deskproNNNNN

> cp -r /var/tmp/laceXXXXX /your/copy

2: Edit acedb files

Now make the following series of alterations to files in the wspec subdirectory:


Edit wspec/passwd.wrm, replace the userids there with your own.

Edit wspec/serverconfig.wrm and replace "READ PASSWD" with "READ WORLD"

3: Edit ZMap files

Copy the file ZMap/ZMap into your .ZMap directory giving it a name something like ZMap.bug_name and make the following alterations:

In the [ZMap] stanza the "sources" keyword gives the name of the reference sequence, make a note of it and:


default-sequence = reference sequence name

comment out show-mainwindow:

#show-mainwindow = false

In the stanza with the reference sequence name change the "url" keyword:


from something like this:


url = acedb://localServer:password@localhost:56879


to this:

url = acedb://any:any@MACHINE:PORT


MACHINE and PORT need to match the machine and port where you run the ace server (see next section).

When you want to run zmap you should copy this file so that zmap will find it automatically when it starts up:


> cp ~/.ZMap/ZMap.bug_name ~/.ZMap/ZMap

4: Start the acedb server

Start the acedb server on your or any other machine on the Sanger network:


for deskpros

> ~acedb/RELEASE.DEVELOPMENT/bin.LINUX_4/sgifaceserver /your/copy PORT 0:0


for the 64 bit cbi4 linux machines, e.g. cbi4g


> ~acedb/RELEASE.DEVELOPMENT/bin.LINUX_64/sgifaceserver /your/copy PORT 0:0

where PORT is a number somewhere between 20000 an 50000

5: Start zmap

Now you should be able to run zmap:


./zmap