ensembl+DAS deployment
I have migrated “ensembl + DAS” from Marie’s linux workstation to Kampen and Genesis successfully. Marie has helped me to do everything from scratch (including hacks on ensembl web codes), so that we...
View ArticleWorkflow Environments Guide
This guide is excerpted from Chris Dwan (Bioteam). Original Link is here . ========================================= I’ve compiled a short list of the features that I use to differentiate these...
View Articlefixed bugzilla perl path in batch
During bugzilla deployment, I found all the scripts hardcoded perl interpreter to be “/usr/bin/perl”. Our current environment uses perl at other locations and this makes deployment difficult if we are...
View ArticleSet timeout for SOAP::Lite
The default HTTP timcout is 180 seconds (3 minutes), but this is not enough for long SQL query or BLAST operations. In some cases, we need to set a longer timeout for SOAP requests. With SOAP::Lite...
View ArticleAdd timestamping support to prozilla-2.0.3
This request is initiated by Mojun to enhance prozilla-2.0.3. We need the function where prozilla will skip downloading a file if the local copy is the same as the remote. She did this for...
View Articlevarchar(byte) vs. varchar(char)
In oracle, varchar2 is widely used to hold variable length string. For varchar data type, there are two minor variants: varchar(byte) and varchar(char). Usually developer does not care about and uses...
View ArticlePrototype code to run batch jobs with SGE
User once ran thousands of “agrep” jobs on our 20 CPU Solaris machine and took all the CPUs. I am leading the process to introduce cluster computing to the bioinformatics group, so this is a good...
View ArticleAbout puzzlebird
So, here is something about me. Expertises: HPC Architecutre, Performance tuning (system/program profile), Linux/Unix, Mac osX, Oracle, MySQL, Perl, C, SHELL, PHP, XML, Joomla Hope: 心有戚戚, 结识同道 My...
View ArticleUse map() to process array
map() is a useful function in PERL to process all the elements in the array. I got one senario that bugs quite some time. I would like to use map() to replace the white space for each element in the …...
View ArticlePerl: “use strict”
Well, if you do not know “use strict” in perl, you are still perl noob. In short, “strict” is a perl module that help you writing neat code. For example, it helps detect un-declared variables, or...
View ArticleAdvance regular expression usage
This notes shows an advanced usage of perl regular expression. There is an array of file names, I need pick up those txt files NOT starting with “abc” and “de”. This could not be done easily with...
View ArticleWindows control “ListBox” datasource refresh
When Windows.Forms.ListBox which is bound to a C# array through its DataSource property, the content of the array displays properly in the listbox. But the content of array is modified, what’s the best...
View ArticleConsuming SRS with Web Service
This documentation was written for a project I did to explore how SRS can help phamaseutical enterprise manage their data and internal developed application. For use or reference, please cite this site...
View ArticleGenerate list of large files in a file system
One of the NFS file system has been reaching 90% watermark from time to time. Although we wrote emails to end users for their help to clean up. The effect is not good enough. To identify the big files...
View ArticleEnsembl mirror inaccessbile under intensive MySQL requests
The background for this issue that our user found local ensembl mirror sometimes inaccessible, but after a few refresh the pages comes out again. I realized the problem was caused by the small default...
View ArticleFixing “morning inaccessible” bug in modperl
There was a strange problem with our ensembl server that usually the server becomes “inaccessible” in the morning, but when we tested a few times, the server works extremely well during the day....
View ArticleEMC storageScope known issue fixed by me
After we migrate the EMC SAN storage to a new SAN device, we found the storageScope graph does not work properly. It can either show the historical data till the migration date, or show the graph from...
View Articleprozilla support for proxy
Proxy 2.0.3+ supports proxy download via http and ftp. It is configured using configuration file, not the option file from command line. The online documentation of prozilla is extremely confusing, so...
View ArticleWhere idea comes from
Excerption from “Art of Project Management” chapter six. “Idea” here means the ‘how” to fulfil the requirements collected in the earlier stage. Additional notes on improvisational game: Yes, and…. When...
View ArticleZT: lousy experience with Nokie
Sounds like quite true… Nokie? I have been using it for a long time. This is a classic example of bad services and bullying. It’s a shame that a strong company like Nokia is rotting to such a level....
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