Local BLAST installation on Linux

[lindashirley99]

Hi everybody,
I am trying to install standalone Blast (blast-2.2.25+) on my linux system. Following the step suggested by this webpage
http://www.ncbi.nlm.nih.gov/books/NBK52640/

After installation and configuration, when I type blastn command, the system always gives this error
-bash: blastn: command not found
even if I type ls,ll some basic unix command, it does't work.

Please help!!!

[GenoMax]

Originally Posted by lindashirley99

Hi everybody,
I am trying to install standalone Blast (blast-2.2.25+) on my linux system. Following the step suggested by this webpage
http://www.ncbi.nlm.nih.gov/books/NBK52640/

After installation and configuration, when I type blastn command, the system always gives this error
-bash: blastn: command not found
even if I type ls,ll some basic unix command, it does't work.

Please help!!!

Lindashirley99,

It appears that you may not be in the right directory where you installed blast. Check where you presently are using the "pwd" command.
If you are in the right directory then that directory is not in your $PATH. You can either amend your $PATH to include the blast directory or specify a "./" before issuing the actual command like so:

prompt> ./blastn

[lindashirley99]

Originally Posted by GenoMax

Lindashirley99,

It appears that you may not be in the right directory where you installed blast. Check where you presently are using the "pwd" command.
If you are in the right directory then that directory is not in your $PATH. You can either amend your $PATH to include the blast directory or specify a "./" before issuing the actual command like so:

prompt> ./blastn

thx so much! You saved me!

[lindashirley99]

Originally Posted by GenoMax

Lindashirley99,

It appears that you may not be in the right directory where you installed blast. Check where you presently are using the "pwd" command.
If you are in the right directory then that directory is not in your $PATH. You can either amend your $PATH to include the blast directory or specify a "./" before issuing the actual command like so:

prompt> ./blastn

Regarding the above issue, is it possible to blast the query sequence just against a user-defined reference, e.g. fasta file of some particular gene sequences, but not the entire genome database?

[rglover]

yes, that's possible - you'll need to create a blast database from the sequences you want to search against:

makeblastdb -in sequences.fasta -dbtype nucl

Then you'd blast as normal, but the name of your database would be sequences.fasta. The BLAST+ user manual is a good place for more information: http://www.ncbi.nlm.nih.gov/books/NBK1763/

[jp.]

Hi
Can someone explain me why I get this errors:
I am using the blast for tophatfusionpost analysis.
I have downloaded:
1. ncbi-blast-2.2.29+
2. nr
3. nt
dir structure is :
wd/ncbi-blast-2.2.29+
wd/blast/nt
wd/blast/nr
PATH=$PATH:wd/ncbi-blast-2.2.29+
PATH=$PATH:wd/blast/nt
PATH=$PATH:wd/blast/nr
export PATH
After that, when I run program,it can not find nt and nr databse.
It gives these 3 errors as follows:
sh: blastn: command not found
blast database error: nt not found in the PATH [wd/blast/nt]
blast database error: nt not found in the PATH [wd/blast/nr]
These nt and nr are in the same PATH, why program can not find it?
I read the blast home page, but can not understand why I get errors?
Kind help is much appreciated.

[atcghelix]

Originally Posted by jp.

Hi
Can someone explain me why I get this errors:
I am using the blast for tophatfusionpost analysis.
I have downloaded:
1. ncbi-blast-2.2.29+
2. nr
3. nt
dir structure is :
wd/ncbi-blast-2.2.29+
wd/blast/nt
wd/blast/nr
PATH=$PATH:wd/ncbi-blast-2.2.29+
PATH=$PATH:wd/blast/nt
PATH=$PATH:wd/blast/nr
export PATH
After that, when I run program,it can not find nt and nr databse.
It gives these 3 errors as follows:
sh: blastn: command not found
blast database error: nt not found in the PATH [wd/blast/nt]
blast database error: nt not found in the PATH [wd/blast/nr]
These nt and nr are in the same PATH, why program can not find it?
I read the blast home page, but can not understand why I get errors?
Kind help is much appreciated.

Try setting an environmental variable $BLASTDB to include the directory that holds your blast database files (instead of including that directory in your $PATH).

Also, if you put those settings in something like your .profile file, then you need to load that file first before your shell will update the environmental variables. The easiest way to do that is by logging out and logging in.

[rhinoceros]

Originally Posted by jp.

Hi
Can someone explain me why I get this errors:
I am using the blast for tophatfusionpost analysis.
I have downloaded:
1. ncbi-blast-2.2.29+
2. nr
3. nt
dir structure is :
wd/ncbi-blast-2.2.29+
wd/blast/nt
wd/blast/nr
PATH=$PATH:wd/ncbi-blast-2.2.29+
PATH=$PATH:wd/blast/nt
PATH=$PATH:wd/blast/nr
export PATH
After that, when I run program,it can not find nt and nr databse.
It gives these 3 errors as follows:
sh: blastn: command not found
blast database error: nt not found in the PATH [wd/blast/nt]
blast database error: nt not found in the PATH [wd/blast/nr]
These nt and nr are in the same PATH, why program can not find it?
I read the blast home page, but can not understand why I get errors?
Kind help is much appreciated.

Read the manual, not the home page. For database paths, you need to create a .ncbirc file to your home where you provide the necessary information.

[jp.]

thank you for kind reply
However, I m new in this field. is it possible to get detail steps for the same. I m using human blast.
I m trying reading blast mannual too.
thank you

[rhinoceros]

Originally Posted by jp.

thank you for kind reply
However, I m new in this field. is it possible to get detail steps for the same. I m using human blast.
I m trying reading blast mannual too.
thank you

http://www.ncbi.nlm.nih.gov/books/NBK52640/

[mastal]

For blast, the executables are usually in a subdirectory called bin,
so what you need to add to your path is

PATH=$PATH:wd/ncbi-blast-2.2.29+/bin

also set the BLASTDB variable as already mentioned by actghelix.