Installation of BLAST+ without root privileges

[EulnayM]

Hi,

I was trying to install BLAST+ as a dependency to an error correction tool SPRAI into a cluster server which I do not have root privileges, I followed through the configuration instruction in http://www.ncbi.nlm.nih.gov/books/NBK52640 and specified the variables for PATH and BLASTDB as follow:

export PATH="$PATH:$HOME/yanlue_l/ncbi-blast-2.2.30+/bin
echo $PATH
output from echo $PATH: /home/yanlue_l/lcl/bin:/home/yanlue_l/lcl/bin:/usr/share/gridengine/bin/lx26-amd64:/usr/lib64/qt-3.3/bin:/usr/NX/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pssc/bin:/opt/openmpi/bin:/opt/torque/bin:/opt/torque/sbin:/home/yanlue_l/bin:/home/yanlue_l/yanlue_l/ncbi-blast-2.2.30+/bin
export BLASTDB="$HOME/ncbi-blast-2.2.30+/db"
echo $BLASTDB
output from echo: $BLASTDB: /home/yanlue_l/ncbi-blast-2.2.30+/db

However, following these steps, I was still unable execute blastn by name from other directory (causing error message of -bash: blastn: command not found) and when test running the error correction tool, it was also shown that attempt to execute blastn has failed. Only when specifying the path to blastn file I can be able to execute blastn.

I have always used software package manager tool (LPM , developed by Masahiro Kasahara) to install BLAST+ when I do not have root permission however LPM wasn't able to perform the configuration of the extracted tarball after the update to BLAST+ 2.2.30.

Can anyone please kindly point out on the steps I have missed on the installation to make it work for the error correction tool (I wasn't trying to start a local blast)? Or the solution to install/configure BLAST+ correctly?

Thanks for the help =)

[GenoMax]

Have you checked to make sure that the blast programs have execute permissions (and also for bin directory, for all)?

[EulnayM]

Have you checked to make sure that the blast programs have execute permissions (and also for bin directory, for all)?

Hi,

Thanks a lot for your kind reply, I checked the permission for all tools in the bin folder, all of them are "rwxr-xr-x", that should mean execute permission for all, is that correct? For the bin directory the permission are "drwxr-xr-x".

Thanks

[GenoMax]

Those permissions look ok. Is this directory ($HOME/yanlue_l/ncbi-blast-2.2.30+/bin) available on the cluster nodes where this job is running? Are you running the cluster jobs using your account (or a different account)?

[EulnayM]

Those permissions look ok. Is this directory ($HOME/yanlue_l/ncbi-blast-2.2.30+/bin) available on the cluster nodes where this job is running? Are you running the cluster jobs using your account (or a different account)?

Hi,

Yes, I am running from the same account and the directory is in my account directory as well. I am unable to execute blastn anywhere else except in the bin folder and the log from the error correction run also shown the same error message (sh: blastn: command not found).

Thanks

[GenoMax]

Hi,

Yes, I am running from the same account and the directory is in my account directory as well. I am unable to execute blastn anywhere else except in the bin folder and the log from the error correction run also shown the same error message (sh: blastn: command not found).

Thanks

Are "which" or "locate" able to find full path for blastn?

[EulnayM]

Are "which" or "locate" able to find full path for blastn?

Hi,

The full path for blastn is still located within the /home/yanlue_l/ncbi-blast-2.2.30+/bin folder when checked using "locate". However, I have solved the issue by obtaining a sudo right and copying the content in bin folder to /usr/local/bin. That solved the problem.

Thanks for the help