Question: (Closed) BLAST+ installation through SSH ,PUTTY
0
gravatar for tcf.hcdg
3.7 years ago by
tcf.hcdg60
European Union
tcf.hcdg60 wrote:

Hello

I know how to installed command line BLAST(2.2.31) previously, I installed and configured it on windows and unuix enviornment (both are working perfectly). But this time I have large amount of sequences for blast therefor I thought to do this through remote server PuTTY / SSH .

I tried to download and configured it as I did in unix. BUT it seems that there is something wrong. 

44227@lidong2:~>wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.2.31+-X64-linux.tar.gz

I put it in a directory wher I want to install and then extracted it  and configured it as follwing:

$ export PATH="PATH:home/tb44227/nobackup/ncbi-blast-2.2.31+/bin"

then I make the directory of db in ncbi-blast-2.2.31+ directory

$mkdir db

then downloaded  the databases from ncbi and swissprot.

tb44227@lidong2:~/nobackup/ncbi-blast-2.2.31+> -bash: blastn: command not found
If '-bash:' is not a typo you can run the following command to lookup the package that contains the binary:
    command-not-found -bash:
-bash: -bash:: command not found

Could you please guide what|s wrong with the installation and configuration process of blast+.

I am absolutely new in SSH and PUTTY. Applogy if I made some mistakes.

Thanks

 

 

 

blast • 1.6k views
ADD COMMENTlink written 3.7 years ago by tcf.hcdg60
export PATH="$PATH:/home/tb44227/nobackup/ncbi-blast-2.2.31+/bin"

             ^     ^

I see two mistakes which mangled your PATH

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by h.mon26k

Hello tcf.hcdg!

We believe that this post does not fit the main topic of this site.

This is not a bioinformatics question, please investigate how to set $PATH correctly!

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.7 years ago by Daniel Swan13k
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