How to download BLAST+ on Centos (6)

Question

[Nelo]

Hi

How to start with installing and downloading NCBI BLAST+ on my Centos?

Steps to follow replies will be helpful

Thank you

[GenoMax]

Technically no installation should be needed.

• Download the executable here (LINK).
• Uncompress tar -zxvf ncbi-blast-2.12.0+-x64-linux.tar.gz
• Add the bin directory to your $PATH - export PATH=$PATH:/path_to/ncbi-blast-2.12.0+/bin

[Nelo]

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

Answer 1

[Michael]

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 Unless your Centos is extremely outdated (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.

[Michael]

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Centos 6 is unfortunately what I meant with extremely outdated.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.

[Nelo]

yes you're right. While updating the version 2.14 glibc on my centos 6, its not going further after configuration step as it is seeking permission (sudo) to copy the file to system directories.

Stuck again...

[GenoMax]

If you followed the steps I had outlined above no installation should be needed. Is that copy of blast not working? You should be able to simply execute blast by running /path_to_dir_w_blast/blastp -h.

[Nelo]

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.

[Michael]

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.

[Nelo]

okie

Tnkq

[Nelo]

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.

[GenoMax]

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.

[Nelo]

okie tnkq I'll go through the link provided