Question: BLAST 2.3.0 Linux
0
gravatar for shiroemonmadeon
3.1 years ago by
shiroemonmadeon0 wrote:

I installed blast 2.3.0 following this guide. But when I run blastn it notified

The program 'blastn' is currently not installed. You can install it by typing: sudo apt-get install ncbi-blast+"

But I want to install Blast 2.3.0, and If I type sudo apt-get install ncbi-blast+ it will install blast 2.2.31

Please Help me.

blast • 1.8k views
ADD COMMENTlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0
0
gravatar for Charles Plessy
3.1 years ago by
Charles Plessy2.6k
Japan
Charles Plessy2.6k wrote:

It looks like you are using Ubuntu or a derivative. On this distribution, the command-line interface will attempt to guess which package to install, if you type the name of a program that is not available.

Available programs are in the directories listed by the command echo $PATH. Therefore, either you need to add in your PATH the blastn program that you compiled, or you need give the full path to your command.

In the documentation that you cited in your question, there are explanations on how to add blastn to you PATH, see here.

ADD COMMENTlink modified 6 months ago by RamRS20k • written 3.1 years ago by Charles Plessy2.6k

Thank you. I use Ubuntu. I did that, but nothing changed. It still notified blastn is not installed :(

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0

Probably the contents of the PATH variable still does not reflect where the blastn file is located.

As an alternative to configure the PATH variable, you can call the program using its absolute path. For instance, if your home directory is /home/shiroemonmadeon, and if you unpacked the ncbi-blast-2.3.0+-x64-linux.tar.gz archive in your home directory, then you would be able to run the blastn program by typing /home/shiroemonmadeon/ncbi-blast-2.3.0+/bin/blastn.

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by Charles Plessy2.6k

I tried. but it didn't run

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0

If you would like efficient help from me or others in this forum, you really need to provide more information, otherwise, nothing can be done. First, what did you download exactly, and where did you unpack that file?

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by Charles Plessy2.6k

I downloaded and unpacked. I installed Blast 2.3.0. My problem: I only run BLAST when I type :

shiroemon@shiroemon:~$ cd /home/shiroemon/
shiroemon@shiroemon:~$ ./ncbi-blast-2.3.0+/bin/blastn -db NewDb -query sample.txt

I want to run Blast without typing ./ncbi-blast-2.3.0+/bin/ before. ie How to run BLAST by openning cmd and type:

shiroemon@shiroemon:~$ blastn -db NewDb -query sample.txt
ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0

In the documentation (the link I gave before), there is the following command:

export PATH=“$PATH:$HOME/ncbi-blast-2.2.29+/bin”

But it needs two changes to make it work: first, correct the version number (2.3.0 instead of 2.2.29), and second replace the typographical quotation marks () by their ASCII equivalent (").

export PATH="$PATH:$HOME/ncbi-blast-2.3.0+/bin"
ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by Charles Plessy2.6k

aaaaa. THANK YOU SO MUCHHHH. The problem is ("). OMG. THANK YOU!!!!!

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by shiroemonmadeon0
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