Batch scripts are missing shebang

[fennerm]

hm.batch* don't have a shebang which causes issues if you call them from outside a bash script e.g from python.

[mapleforest]

Dear User,

HM2 is not designed to be run in that way, but you may modify it to suit your application.

在 2017/11/30 3:13, fennerm 写道:

hm.batch* don't have a shebang which causes issues if you call them from outside a bash script e.g from python.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

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[fennerm]

Fair enough. Is there any downside to adding the shebang though? Writing a custom batch script in perl or python seems like a fairly common use case.

[mapleforest]

I do not think so, but I did not test that.

The batch scripts just automated the perl scripts under HM2/bin, read though them and you know what they do. However, everything is supposed to run in a project directory under HM2's root directory. Besides, scripts under HM2/bin do not have the FindBin.

在 2017/11/30 7:56, fennerm 写道:

Fair enough. Is there any downside to adding the shebang though? Writing a custom batch script in perl or python seems like a fairly common use case.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

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[fennerm]

I understand, I'm talking about replacing the main batch script with a perl or python script. If these scripts then try to execute the hm.batch* scripts they will not necessarily default to executing them with bash without a shebang. Instead they will use the user's default shell which may be zsh etc.

If you're not interested in changing it, no problem. Just wanted to bring it to your attention in case it was unintentional. Thanks for developing Haplomerger2, very useful software!

[mapleforest]

Thank you. As you can see in the manual, I recommend explicit invocation with "sh ./hm.batch*".

I do this for reasons I explained above.

But I am sure for users who have highly customized demands, can easily adapt HM2 by modifying a couple of lines.

Feel free to contact me if you have any technical problems.

在 2017/12/1 5:46, fennerm 写道:

I understand, I'm talking about replacing the main batch script with a perl or python script. If these scripts then try to execute the hm.batch* scripts they will not necessarily default to executing them with bash without a shebang. Instead they will use the user's default shell which may be zsh etc.

If you're not interested in changing it, no problem. Just wanted to bring it to your attention in case it was unintentional. Thanks for developing Haplomerger2, very useful software!

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

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