troubles in installation

Choi Baeyoung

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Dec 2, 2022, 6:34:40 AM12/2/22

to GetOrganelle

Hi, I'm working on plant big data analysis.

I'd like to assemble the chloroplast genome from short-read data but I was faced with trouble in installation.

I used the conda environment to install getorganelle in CentOS Linux release 8.5.2111.

When I try to set up GetOrganelle Database using "get_organelle_config.py", I faced an error as follows.

(getorganelle) [root@localhost ~]# get_organelle_config.py

Python 3.8.15 (default, Nov 24 2022, 15:19:38) [GCC 11.2.0]
ERROR: Blast is not available!
(getorganelle) [root@localhost ~]# get_organelle_config.py --add embplant_pt,embplant_mt

Python 3.8.15 (default, Nov 24 2022, 15:19:38) [GCC 11.2.0]
ERROR: Blast is not available!

I checked the post on GitHub and then installed libgomp.x86_64 using yum, but I cannot fix the problem.

Would you please help me?

Sincerely,

jj3111

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Dec 2, 2022, 4:18:05 PM12/2/22

to GetOrganelle

Could you provide the information when you type in

blastn

at terminal?

Choi Baeyoung

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Dec 5, 2022, 6:15:23 AM12/5/22

to GetOrganelle

At terminal, I can operate blastn commend.

At the conda environment, I figured out an error for using blastn as below.

(getorganelle) [root@localhost ~]# blastn
blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory

To solve this, I installed libnsl using yum and then finally I can operate the getorganelle command.

Thank you for your kind comments on figuring out problems!

Sincerely,

2022년 12월 3일 토요일 오전 6시 18분 5초 UTC+9에 jj3111님이 작성:

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