How to configure my database to wwwblast?

Question

[Sathish]

Dear all,

I am using wwwblast-2.2.25 for setting up local blast in CentOS. As per instructions I have moved my database files to “blast/db” folder and altered “blast.rc” and “blast.html” files. It was worked fine by localhost blast page. At present I want to know that, is it possible to give path link or symbolic link to access my database which present in other directory (not moved in “blast/db”).

Note: blast.rc shows that

Format: <program> <db> <db> ...

blastn db1 db2 ..

Can anybody tell me how to resolve this?

Thanks

Answer 1

[Devon Ryan]

Certainly, in fact it's often more convenient to create symlinks to directories holding the databases rather than copying/moving the databases themselves. Here's what I see when I look at some of our blast databases (note, this is running in a Docker container and I've changed some names, which will explain why things look a bit weird):

root@4f4e26d406ab:/var/www/html/blast/db# ls -l
total 76
lrwxrwxrwx. 1 root root   42 Jul  8 07:27 Lib_A243_ALL -> /data/fish_WGS/A243/readDB/Lib_A243_ALL
lrwxrwxrwx. 1 root root   40 Jun 29 13:53 Lib_A243_B -> /data/fish_WGS/A243/readDB/Lib_A243_B
lrwxrwxrwx. 1 root root   40 Jun 29 13:53 Lib_A243_G -> /data/fish_WGS/A243/readDB/Lib_A243_G
lrwxrwxrwx. 1 root root   40 Jun 29 13:53 Lib_A243_K -> /data/fish_WGS/A243/readDB/Lib_A243_K

[Sathish]

Thanks for your reply. As per wwwblast manual shows that, the database should be the following order.

blast program db1 db2 ..

Here db1 and db2 are my databases those files are in db folder. If I want to assign third database (db3) from other directory how shall I?

[Devon Ryan]

".." and "..." generally means "and so on". So just add it after db2. You can also just spread things over multiple lines:

blast program db1
blast program db2
...