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CSB5 / lofreq

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http://csb5.github.io/lofreq/
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I have trouble to run bootstrap #113

Closed ryao-mdanderson closed 3 years ago

ryao-mdanderson commented 3 years ago

Hello:

I attempted to build lofreq 2.1.5 for our users on RHEL 7.4 system. By review README, I have the followings in path: module load python/3.7.3-anaconda module load htslib/1.10.2 our system has zlib-devel rpm installed

I git clone the source code for this site, however, ./bootstrap command hung, I only notice that autom4te.cache directory has a time stamp change but nothing else.

May you please point out the possibly reasons and provide suggestion?

Thank you in advance. Rong

ryao-mdanderson commented 3 years ago

More information to add on: I use gcc version 7.1.0; I tried both Redhat 7.4 and 7.9, bootstrap hung.

andreas-wilm commented 3 years ago

Hi Rong, I've never heard of this issue before. This should either fail or work, but hanging sounds like a difficult to debug problem. You could try your luck with running bootstrap with strace.

Is there a reason you need to install from source or are Conda / Linuxbrew an alternative for you?

ryao-mdanderson commented 3 years ago

Hi Andreas,

Thank you for your quick response. I followed the readme in github https://github.com/CSB5/lofreq, thus I thought I have to build from source for version 2.1.5. After reading your reply, I just tried installed lofreq by conda environment. It works!

I appreciate your help. Rong

From: Andreas Wilm @.> Reply-To: CSB5/lofreq @.> Date: Monday, April 5, 2021 at 8:53 PM To: CSB5/lofreq @.> Cc: "Yao,Rong" @.>, Author @.***> Subject: [EXT] Re: [CSB5/lofreq] I have trouble to run bootstrap (#113)

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Hi Rong, I've never heard of this issue before. This should either fail or work, but hanging sounds like a difficult to debug problem. You could try your luck with running bootstrap with strace.

Is there a reason you need to install from source or are Conda / Linuxbrew an alternative for you?

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