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: $BLASTDB: /home/yanlue_l/ncbi-blast-2.2.30+/db
However, following these steps, I was still unable execute blastn by name from other directory (causing error message of -bash: blastn: command not found) and when test running the error correction tool, it was also shown that attempt to execute blastn has failed. Only when specifying the path to blastn file I can be able to execute blastn.
I have always used software package manager tool (LPM , developed by Masahiro Kasahara) to install BLAST+ when I do not have root permission however LPM wasn't able to perform the configuration of the extracted tarball after the update to BLAST+ 2.2.30.
Can anyone please kindly point out on the steps I have missed on the installation to make it work for the error correction tool (I wasn't trying to start a local blast)? Or the solution to install/configure BLAST+ correctly?
Thanks for the help =)
I was trying to install BLAST+ as a dependency to an error correction tool SPRAI into a cluster server which I do not have root privileges, I followed through the configuration instruction in http://www.ncbi.nlm.nih.gov/books/NBK52640 and specified the variables for PATH and BLASTDB as follow:
export PATH="$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 =)
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