ModuleNotFoundError: No module named 'pypiper'

qiaowei-vvjoe commented 5 years ago

Hi I am now test this PEPATAC pipline.I install pypiper python package by miniconda3,but when I test the pepatac.py without looper it shows No module named 'pypiper'.Could anyone help me with the error?Thanks so much in advance.

nsheff commented 5 years ago

What command did you use to install?

On pypi, the pypiper package is called piper (not pypiper).

qiaowei-vvjoe commented 5 years ago

@nsheff Hi I am so sorry for that stupid question but I just test the pepatac.py.

python3 pepatac.py -P 5 -O /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/example/data -S test_without_looper -G hg38 -Q paired -C pepatac.yaml -gs hs -I /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/examples/data/test1_r1.fastq.gz -I2 /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/examples/data/test1_r2.fastq.gz

nsheff commented 5 years ago

Hi, you're not installing pypiper correctly. this shows how to install it:

http://pypiper.databio.org/en/latest/

qiaowei-vvjoe commented 5 years ago

Hi @nsheff I just wget https://github.com/databio/pypiper/archive/v0.12.0.zip then unzip v0.12.0.zip then go to pypiper-0.12.0/example_pipelines to test python3 hello_pypiper.py

but it still showed No module named 'pypiper' did I do any wrong steps? I am so sorry for that stupid question.

nsheff commented 5 years ago

you have not installed pypiper. please install pypiper first. please read my earlier comments.

qiaowei-vvjoe commented 5 years ago

@nsheff Hi Nathan I have installed pypiper according to your comment and run python3 hello_pypiper.py successfully.

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Elapsed time (this run): 0:00:01
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Peak memory (this run): 0 GB
Pipeline completed time: 2019-08-17 10:03:27

But when I test the example there comes other errors, for me now I just know the line36. The examples/data/test1 is come from the PEPATAC. Could you please give me a help for this problem?I am so sorry for these too much questions.Thank you so much.

$ python3 pepatac.py -P 5 -O /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/examples/data -S test1_without_looper -G hg38 -Q paired -C pepatac.yaml -gs hs -I /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/examples/data/test1_r1.fastq.gz -I2 /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/examples/data/test1_r2.fastq.gz

Traceback (most recent call last): File "pepatac.py", line 1422, in sys.exit(main()) File "pepatac.py", line 461, in main args = parse_arguments() File "pepatac.py", line 36, in parse_arguments required=["input", "genome", "sample-name", "output-parent"]) File "/mnt/disk1/qiaowei/miniconda3/lib/python3.7/site-packages/pypiper/utils.py", line 60, in add_pypiper_args argument_groups=groups, arguments=args, use_all_args=all_args) File "/mnt/disk1/qiaowei/miniconda3/lib/python3.7/site-packages/pypiper/utils.py", line 808, in _determine_args from logmuse import LOGGING_CLI_OPTDATA ImportError: cannot import name 'LOGGING_CLI_OPTDATA' from 'logmuse' (/mnt/disk1/qiaowei/miniconda3/lib/python3.7/site-packages/logmuse/init.py)

jpsmith5 commented 4 years ago

Did you have any more luck with this @qiaowei-vvjoe? I can run your command, modified for my file system successfully.

From the pepatac parent folder:

python3 pipelines/pepatac.py -P 5 -O /project/shefflab/pepatac_tutorial/data -S test1_without_looper -G hg38 -Q paired -C $CODE/pepatac/pipelines/pepatac.yaml -gs hs -I $CODE/pepatac/examples/data/test1_r1.fastq.gz -I2 $CODE/pepatac/examples/data/test1_r2.fastq.gz

Which version of the pipeline were you attempting here? Most recent version should be 0.9.5.

jpsmith5 commented 4 years ago

If you have another issue in this line of questioning please let us know @qiaowei-vvjoe

qiaowei-vvjoe commented 4 years ago

I am very sorry that I have left the place where I worked last year without solving this problem , but still thank you very much for your help.I will test it again according to your command.

------------------ 原始邮件 ------------------ 发件人: "databio/pepatac" <notifications@github.com>; 发送时间: 2020年9月15日(星期二) 凌晨3:03 收件人: "databio/pepatac"<pepatac@noreply.github.com>; 抄送: "乔玮"<1270885824@qq.com>;"Mention"<mention@noreply.github.com>; 主题: Re: [databio/pepatac] ModuleNotFoundError: No module named 'pypiper' (#122)

Did you have any more luck with this @qiaowei-vvjoe? I can run your command, modified for my file system successfully.

From the pepatac parent folder: python3 pipelines/pepatac.py -P 5 -O /project/shefflab/pepatac_tutorial/data -S test1_without_looper -G hg38 -Q paired -C $CODE/pepatac/pipelines/pepatac.yaml -gs hs -I $CODE/pepatac/examples/data/test1_r1.fastq.gz -I2 $CODE/pepatac/examples/data/test1_r2.fastq.gz
Which version of the pipeline were you attempting here? Most recent version should be 0.9.5.

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databio / pepatac

ModuleNotFoundError: No module named 'pypiper' #122

Pipeline completed. Epilogue