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jjmiao1314 / 16sPIP

16sPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on 16S Metagenomic Sequencing
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possible bug in installation script #2

Open ARW-UBT opened 3 years ago

ARW-UBT commented 3 years ago

Hello, I have installed 16sPIP as described in the help instruction on the www pages. For some reasons, there seems to be in typo in the installation script. Two folders seem not receive the folder name as expected: These are

/bin/6sPIP_BIN /bin/6sPIP_PATH Is this as typo (I would expect 16sPIP... instead of 6sPIP...)

The example scripts give in the help menu do not complete sucessufully, the reason could be this type described above. Do I have to adjust the REF_PATH on line 20 in 16sPIP.sh? I have attached the content of /bin and a log file of your example:

Thanks for your suppor log2.txt log1.txt t!

Mr-Wornock commented 3 years ago

Have you solved the problem yet?

ARW-UBT commented 3 years ago

Yes, I have resolved the issue by manually correcting the bugs in the installation script. Best regards

Mr-Wornock commented 3 years ago

Could you tell me your solution? I have met the same problem and haven't solved it yet，thank you❤️

发自 网易邮箱大师

---- 回复的原邮件 ---- | 发件人 | @.> | | 日期 | 2021年11月10日 18:33 | | 收件人 | @.> | | 抄送至 | @.**@.> | | 主题 | Re: [jjmiao1314/16sPIP] possible bug in installation script (#2) |

Yes, I have resolved the issue by manually correcting the bugs in the installation script. Best regards

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ARW-UBT commented 3 years ago

I do not have tracks of the steps. But what I did was to look at the error messages produced by the installer.sh scripts and try to get this issue resolved by adaptung to the local machine. One important step was to manually copy any of the produced *.sh scripts also to the /bin/ folder (this is one bug in the script). I am not sure whether it made any difference, but I used a fresh virtual installation of Ubuntu 16.04 as 16sPIP has been developed on this version. I was not successful on CentOS7 and Ubuntu 18.04

Best regards ALfns

Mr-Wornock commented 3 years ago

Thank you for your kind attention personal response.

Best regards

ericbrzoska commented 1 year ago

Does anyone found an alternative tool?

ARW-UBT commented 1 year ago

Hi @ericbrzoska have a look at FAPROTAX, it has some pathogenic bacteria in its database.