Troubleshooting installation of BLAST+

[AGL]

Hi!

I've got a copy of ncbi-blast-2.2.30+.dmg. The installer runs as expected and reports successful installation to my HD. However, I then can't find the application anywhere on my HD.

What's up?

I have an Administrator account on a Mac running OS X 10.10.2.

Any advice would be most welcome.

Thanks in advance.

[GenoMax]

In "/usr/local/ncbi/blast/bin".

Even though installer has a GUI you will need to run blast using command line in a terminal.

[AGL]

Thanks for your reply.

Apologies as I should have also said in my earlier post that I've checked, both through the Terminal and through the Finder, and it seems I don't have a file of directory named 'Local'.

Still no Blast+.

[GenoMax]

Can you try making a directory called local in /usr (I had one from a different install)? Blast may assume that the directory exists (it does on linux where blast development likely occurs). I am surprised that the installer did not throw an error.

Are you doing the install from an account that has admin privileges?

[AGL]

Thanks again for your reply.

I tried as you suggested but had the same result. The /Local (or /local) folder remains empty even though the installer says everything went well.

Very frustrating.

[AGL]

BTW: I am running as Administrator on my machine.

[GenoMax]

Directory needs to be under /usr (not as /local). You will have to do

$ sudo mkdir /usr/local
$ sudo mkdir /usr/local/ncbi
$ sudo mkdir /usr/local/ncbi/blast

Is this where you made the directories?

[AGL]

I did it in Finder at my home folder. I haven't made subfolders for ncbi or blast.

Hopefully that wasn't a #facepalm I just heard from over there.

I assume usr is my user name as it appears on my home folder?

[GenoMax]

Hopefully that wasn't a #facepalm I just heard from over there.

I assume usr is my user name as it appears on my home folder?

"usr" is a real system directory (off the root "/" partition). It is NOT your user account directory. Issue the commands I posted above from a terminal window (you will need to provide your password again, you said you have admin privileges on your account).

If /usr does not exist on your machine then make that directory first.

$ sudo mkdir /usr

[AGL]

I ran through all sudo commands. In all cases the terminal returned 'File exists'

I hate to say I don't get it but I don't. Guess I've got a lot of reading to do on basic Terminal commands before I can access BLAST.

Thanks for taking the time.

[GenoMax]

Can you do the following (in a terminal window) and tell us what happens?

$ ls -l /usr/local/ncbi/blast/bin

$ /usr/local/ncbi/blast/bin/blastn -help

I have a feeling you have the programs installed (if you are getting that files exists message).

[AGL]

Yep.

However, this is what I get from the bin:

Sebastians-iMac:~ Seb$ ls -l /usr/local/ncbi/blast/bin
total 1527440
-rwxrwxr-x 1 3755 5333 46133784 27 Oct 23:09 blast_formatter
-rwxrwxr-x 1 3755 5333 28238464 27 Oct 23:09 blastdb_aliastool
-rwxrwxr-x 1 3755 5333 32282276 27 Oct 23:09 blastdbcheck
-rwxr-xr-x 1 3755 5333 40530656 27 Oct 23:09 blastdbcmd
-rwxr-xr-x 1 3755 5333 46121556 27 Oct 23:08 blastn
-rwxr-xr-x 1 3755 5333 46113260 27 Oct 23:08 blastp
-rwxr-xr-x 1 3755 5333 46113260 27 Oct 23:08 blastx
-rwxrwxr-x 1 3755 5333 29698756 27 Oct 23:09 convert2blastmask
-rwxrwxr-x 1 3755 5333 46369232 27 Oct 23:09 deltablast
-rwxr-xr-x 1 3755 5333 29935496 27 Oct 23:09 dustmasker
-rwxr-xr-x 1 3755 5333 51345 28 Jun 2010 legacy_blast.pl
-rwxr-xr-x 1 3755 5333 32293864 27 Oct 23:09 makeblastdb
-rwxr-xr-x 1 3755 5333 31012976 27 Oct 23:09 makembindex
-rwxrwxr-x 1 3755 5333 30376380 27 Oct 23:09 makeprofiledb
-rwxr-xr-x 1 3755 5333 46208788 27 Oct 23:08 psiblast
-rwxr-xr-x 1 3755 5333 46180436 27 Oct 23:09 rpsblast
-rwxr-xr-x 1 3755 5333 46180440 27 Oct 23:09 rpstblastn
-rwxr-xr-x 1 3755 5333 30537996 27 Oct 23:09 segmasker
-rwxr-xr-x 1 3755 5333 46171672 27 Oct 23:08 tblastn
-rwxr-xr-x 1 3755 5333 46113260 27 Oct 23:08 tblastx
-rwxrwxr-x 1 3755 5333 12486 11 Sep 2014 update_blastdb.pl
-rwxr-xr-x 1 3755 5333 35312540 27 Oct 23:09 windowmasker

Check the dates. Do I actually have a legacy version installed?

The -help command you sent through didn't work (No such file or directory).

I ran the uninstaller before re-running the installer.

[AGL]

Actually, scratch that last.

All good.

Found the help file.

Thanks heaps!

[GenoMax]

Indeed the programs are installed! You have the latest version (that is when they were built at NCBI).

What I don't understand is why you did not get an output for -help command. If you copied and pasted the command from above then do not copy the leading $. Your file permissions look correct so you should get help for blastn printed to screen. Try again.

[AGL]

Yes, found it. Typographical error.

Thanks very much for all your help.