Hi
How to start with installing and downloading NCBI BLAST+ on my Centos?
Steps to follow replies will be helpful
Thank you
Hi
How to start with installing and downloading NCBI BLAST+ on my Centos?
Steps to follow replies will be helpful
Thank you
I don't know which version of Centos you have, but try with Bioconda. Unless your Centos is extremely outdated (<= Centos 6), it should be the easiest way. For step-by-step instructions follow the Bioconda documentation.
If you are running an unsupported version of Centos (<=6) with glibc version < 2.14 you cannot run most recent software. Besides, you are facing a security hazard (no security updates). Update to at least Centos 7.
There was a comment here for a short time mentioning Centos version 6 but then it was deleted.
Centos 6 is unfortunately what I meant with extremely outdated. We had a box with Centos 6 here too, it is possible to install a newer version of Glibc (at least 2.14)and you need a custom built setup but it turned out to be extremely cumbersome to maintain and you need support from your sysadmin to install it. I highly recommend to update at least to Centos 7 instead. Older Centos and bleeding edge scientific software don't go well together.
I followed your step mentioned above and BLAST is installed. But now I trying to create a local database using multiple fasta files using command given below:
makeblastdb –in seq.fa –dbtype prot –parse_seqids
Using this command, displayed the below result on my terminal:
makeblastdb: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by makeblastdb)
asking for glibc 2.14 for makeblastdb command.
This is a problem with Centos 6, it is so old that most 'modern' software (including software installed via conda) does not run because it requires at least glibc 2.14 (GLIBC_2.14 is a symbol that indicates this compatibility). glibc 2.14 cannot be installed from the centos repos, but needs a third party repo or build it from source (I am not going to show how and I am not even sure that still works. You will find a solution easily but I promise you, you are not going to be happy with that). Centos 6 is out of Maintenance/support, if you are still running it, consider upgrading to at least Centos 7, better 8 your first priority.
I change my workstation to an another system in which I have ubuntu 20.04 installed in virtual box.
~/Downloads/ncbi-blast-2.12.0+/bin$ makeblastdb -in seq.fa -dbtype prot -parse_seqids
Command 'makeblastdb' not found, but can be installed with:
sudo apt install ncbi-blast+
Here in bin directory if I list it, makeblastdb is there but whenever I try the command above, command 'makeblastdb' can's be found being displayed.
Please learn some basics of using linux command line. I recommend you spend some time on: https://swcarpentry.github.io/shell-novice/
This is the classic $PATH
issue where the directory you are in is not in system PATH.
For now this should work:
./makeblastdb -in seq.fa -dbtype prot -parse_seqids
You can change the $PATH
variable by export PATH=$PATH:/path_to_blast_bin_dir
.
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Technically no installation should be needed.
tar -zxvf ncbi-blast-2.12.0+-x64-linux.tar.gz
bin
directory to your$PATH
-export PATH=$PATH:/path_to/ncbi-blast-2.12.0+/bin
Hi!
Thanks for replying
I have followed this steps Do You know how to execute the balstp?
AND
I have multiple FASTA files with multiple protein sequences in each and am trying to BLAST for which first I think I need to make a database. So do you know how to make a blast database by using the fasta sequeces i have.
Or
Any other suggestion to carry on this kinda work
Thanks