Orthologous references

Lee, Y., R. Sultana, et al. (2002). “Cross-Referencing Eukaryotic
Genomes: TIGR Orthologous Gene Alignments (TOGA).” Genome Res. 12(3):
493-502.

Mushegian, A. R., J. R. Garey, et al. (1998). “Large-Scale Taxonomic
Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous
Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes.”
Genome
Res. 8(6): 590-598.

Ouyang, M., J. Case, et al. (2003). “Five Hundred Sixty-Five Triples of
Chicken, Human, and Mouse Candidate Orthologs.” Journal of Molcular
Evolution 57(3): 271-281.

rsync

Tutorial copied from http://www.abbeyworkshop.com/howto/unix/nix_rsync/

Using rsync to Mirror Directories

The rsync utility can be used to mirror a directory locally or over a network. As the name implies, rsync synchronizes two directories. Key benefits of the utility include:

* After the first copy, only differences in files are copied, not the entire file. This saves time and bandwidth.
* rsync works with ssh so it can copy files securely over a network.

Command Basics and the slash

To copy a directory from one directory to another, they command line would be:

rsync -options –otherOptions sourceDir targetDir

Example 1: rsync -vaz ~/bk/ ~/test

This example copies the contents of the ~/bk directory to the test test directory.

Example 2: rsync -vaz ~/bk ~/test

This example creates a bk directory under the ~/test directory and recursively copies the contents of the ~/bk into this new directory. This is slighly different from the first example.
Command Line Options

A few command line options are listed in the previous example. Each of these options is described below.
Key rsync Options Option Description
-v Turn on verbose mode
-a This turns on archive mode. Bascially this causes rsync to recurse the directory copying all the files and directories and perserving things like case, permissions, and ownership on the target. (Note: Ownership may not be preserved if you are not logged in as the root user.)
-z Turns on compression during the transfer. This option compresses the data as it is copied over the network.
Copying over ssh

To use ssh to copy the files over the network, just add the –rsh option to the command line. Simply specify the ssh command line as shown in the example. Also, to specify another machine as a target, precede the directory target with a host name and a colon.

Example 3: rsync -vaz –rsh=”ssh -l username” ~/bk targetHost:~/test

After typing the command line, you will be prompted for your password. After entering the password, the command executes and your files are copied. You can also set the ssh command using the RSYNC_RSH environment variable. You can also avoid entering the ssh password if you use ssh keys.
The –exclude Option

This option allows you to exclude certain files and directories from the copy process. You can exclude by specific names or by using wildcards.

Example 4: rsync -vaz –exclude=log/ –exclude=*.xml ~/bk targetHost:~/test

In this example, the log directory is excluded from the copy as well as any file with a .xml extension.
The –delete Option

This option deletes any files that exist in your target directories but that do not exist in the source directory struction. Using this option truly keeps your files synchronized. However, use this option with caution. It can delete a lot of stuff on the target machine if you aren’t careful.

Install apache proxy module in cpanel

cp -p /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.20050509
cd /home/cpins/installd/buildapache/apache_1.3.33/src/modules/proxy
/usr/local/apache/bin/apxs -c mod_proxy.c
/usr/local/apache/bin/apxs -i -a -n proxy mod_proxy.so

Upgrade phpBB forum

1) Download the full package from http://www.phpbb.com/downloads.php, unpack it to a temporary folder, say, /tmp/phpBB2

2) Copy the new package to a temporary folder
$ cp -R /tmp/phpBB2 ppp

3) Copy the old config.php file
$ cp forum/config.php ppp

4) Install the new package: point the browser to http://mydomain.com/ppp/install/update_to_latest.php

5) Remove the install/ and contrib folder
$ rm -rf ppp/install/ ppp/contrib/

6) Copy chinese language package
$ cp -R forum/language/lang_chinese_simplified/ ppp/language

7) Modify logo location, and replace it with the correct logo
$ vi forum/templates/subSilver/overall_header.tpl ppp/templates/subSilver/overall_header.tpl
and search key word logo to find the correct line

8) Copy the Avitar folder
$ cp -R forum/images/avatars/gallery/Avatar_pack_1/ ppp/images/avatars/gallery/

9) Test the new forum at http://mydomain.com/ppp. Remove the old folder if everything looks fine
$ mv forum /tmp/forum.mydomain; mv ppp forum

10) To fight spam registration, I also changed the keyword “agreed” in all files to some other word.