Environment error (no module named peakutils)

Tine-dk commented 3 years ago

Hi,

First, I noticed that when creating the environment the following path does not exist: cd bin/scripts/UnsymmetricPairAlignment

I think you have renamed it to the following: bin/RepeatHMM_scripts/UnsymmetricPairAlignment

Second, I get the following error when trying to run RepeatHMM with a BAM-file as input:

Traceback (most recent call last):
  File "repeatHMM.py", line 11, in <module>
    import peakutils
ModuleNotFoundError: No module named 'peakutils'

When I install peakutils inside the env it still persists that there is no module named peakutils.

liuqianhn commented 3 years ago

@Tine-dk peakutils is a python package. If you created an env for RepeatHMM, please install it in under RepeatHMM env by conda or by pip. It will help me to give more specific suggestions if you share your commands. I did rename bin/scripts/UnsymmetricPairAlignment to bin/RepeatHMM_scripts/UnsymmetricPairAlignment. Thanks for pointing this out. I will make the correction.

huangyuanf commented 3 years ago

Hi, when i run repeatHMM,I get the same erro,when I install peakutils inside the env it still persists that there is no module named peakutils.how can I resolve it.Thanks!

liuqianhn commented 3 years ago

Hi @huangyuanf How do you install the dependent package. Did you install them according to the instructions [here]](https://github.com/WGLab/RepeatHMM/blob/master/docs/Install.md)?

huangyuanf commented 3 years ago

I cp -r "/lustre/huangyf/software/RepeatHMM/" "/lustre/huangyf/software/Miniconda3/envs/repeathmmenv/lib/python2.7/site-packages/" then I run the RepeatHMM as follow:"/lustre/huangyf/software/Miniconda3/envs/repeathmmenv/bin/python2.7" "/lustre/huangyf/software/Miniconda3/envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/bin/repeatHMM.py" BAMinput --Onebamfile "/lustre/huangyf/out/ngmlr.out/sort.bam/20190329-BNP0832-P4-A1.sort.bam" --repeatName all --hg 38 --hgfile "/lustre/huangyf/genome/hg38/ucsc.hg38.fa" --Patternfile "/lustre/huangyf/software/Miniconda3/envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/bin/reference_sts/hg38/hg38.trf.bed" I got erro information: ('No pa file ', '/lustre/huangyf/software/Miniconda3/envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/reference_sts//38/38.predefined.pa')

and I have installed RepeatHMM according to the instructions [here]](https://github.com/WGLab/RepeatHMM/blob/master/docs/Install.md)

and when I run with --Patternfile .pa file Ican got a correct result.

Can you help me where wrong with a bed file?

------------------ 原始邮件 ------------------ 发件人: "WGLab/RepeatHMM" @.>; 发送时间: 2021年6月1日(星期二) 上午10:13 @.>; @.**@.>; 主题: Re: [WGLab/RepeatHMM] Environment error (no module named peakutils) (#35)

Hi @huangyuanf How do you install the dependent package. Did you install them according to the instructions [here]](https://github.com/WGLab/RepeatHMM/blob/master/docs/Install.md)?

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Environment error (no module named peakutils) #35