search

WeichenZhou / PALMER

Pre-mAsking Long reads for Mobile Element inseRtion
MIT License
12 stars 5 forks source link

Installing erro #19

Closed huangyuanf closed 2 years ago

huangyuanf commented 2 years ago

Describe the bug When I installed samtools=1.8,gif-lfs by conda ,I installed ncbi-blast-2.12.0+ by downloaded its code, then I installed PALMER 1.6 by downloading codes in this page！when I run /lustre/huangyf/software/PALMER-1.6/PALMER --input /lustre/huangyf/HG002/HG002-ONT-60X/Hg002.ONT.minimap2/Hg002.ONT.minimap2.bam/Hg002.sort.bam --workdir /lustre/huangyf/HG002/TE.out/mi-palmer-TE/ONT/LINE/ --output /lustre/huangyf/HG002/TE.out/mi-palmer-TE/ONT/LINE/output.prefix --ref_ver GRCh38 --type LINE --ref_fa /lustre/huangyf/HG002/genome/ucsc.hg38.fa I got such information: blastn:command not found when I run blastn only it can run well,so could you help resolve it?Thanks very much

WeichenZhou commented 2 years ago

Hi @huangyuanf,

Thank you for using PALMER. Where did you install blastn? Can you call blastn by using command line 'blastn' by default in your system?

Thanks!

WeichenZhou commented 2 years ago

Please make sure you can run blastn outside of PALMER and you run PALMER in the same environment as blastn.

Thanks!