BLAST Command Line - restarting
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6.5 years ago
t.kranenburg ▴ 40

Recently I installed BLAST for command line on Windows (see code below), and this works.

However, when I restart the command-line prompt, the command blastn does not work immediately, unless I go back to the actual folder and then issue the command. The same applies for setting up a local database; I have to re-run the code which sets up the database. Therefore I was wondering how load the BLAST functionalities and objects into the command line immediately instead of redoing the work.

#Command line BLAST
#Download BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
#Install: ncbi-blast-2.7.1+-win64.exe
#Save test.fasta in  C:\Program Files\NCBI\blast-2.7.1+
cd C:\Program Files\NCBI\blast-2.7.1+
blastn -version
blastn -db nr -query test.fasta -remote -out test_query.txt
blast command line • 4.7k views
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6.5 years ago
ashish ▴ 680

You need to put the blast/bin folder location in your path variable. see this for instructions.

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Thank you for your answer. Is there a way to set the path variable through R, or do I really to go to system-settings (for windows)?

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You need to go to the system settings, add the blast/bin folder to the path variable after which blast can be used from cmd without typing the full address. I don't know of any way to set path variable in R. However, this might be of some help to you.

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6.2 years ago
t.kranenburg ▴ 40

I have tried to set the system path by adding to system path to the NCBI-folder in which BLAST is located. However, it is still not recognized. I guess I'm doing something wrong, but I cannot figure out what yet. Do you have some advice?

Path settings

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You need to add to the PATH variable not in comSpec. You have blast folder mention in your PATH variable but its not complete. use C:\Program Files\NCBI\blast-2.7.1+\bin . In the second picture, PATH is there, edit it.

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I assume that switching to a linux environment is not an option? :-)

(it would be my preferred option though)

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6.1 years ago
t.kranenburg ▴ 40

Fixed it by:

set PATH=%PATH%;C:\Program Files\NCBI\blast-2.7.1+\bin
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