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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Running lofreq_star-2.1.5_linux-x86-64 on Linux 3.10.0-862.3.3.el7.x86_64 x86_64 #100

Open HagenC opened 3 years ago

HagenC commented 3 years ago

Hi and thank you for developing lofreq.

According to your blog: _Download the binary LoFreq distribution matching your system (e.g. Linux or MacOSX) from the dist folder on Github and unpack it. LoFreq can then simply be called with ./lofreqstar-2.1.0/bin/lofreq (assuming you downloaded version 2.1.0). You can move the folder anywhere you like (just preserve its structure) or copy its contents to a system-wide installation path, e.g. /usr/local

When I try ofreq_star-2.1.5_linux-x86-64 i get the error message: ./lofreq: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or director

lofreq_star-2.1.0 works as described in the blog.

What could be the issue?

andreas-wilm commented 3 years ago

Hello, htslib is not statically built into this binary, i.e. you need to install htslib as well for example with Conda. If this install into a non-standard location you will have to set LD_LIBRARY_PATH as well. I keep this open as a reminder to build the next binary differently

Andreas

On Tue, 21 Jul 2020 at 15:09, HagenC notifications@github.com wrote:

Hi and thank you for developing lofreq.

According to your blog: Download the binary LoFreq distribution matching your system (e.g. Linux or MacOSX) from the dist folder on Github and unpack it. LoFreq can then simply be called with ./lofreq_star-2.1.0/bin/lofreq (assuming you downloaded version 2.1.0). You can move the folder anywhere you like (just preserve its structure) or copy its contents to a system-wide installation path, e.g. /usr/local

When I try ofreq_star-2.1.5_linux-x86-64 i get the error message: ./lofreq: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or director

lofreq_star-2.1.0 works as described in the blog.

What could be the issue?

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-- Andreas Wilm andreas.wilm@gmail.com | 0x7C68FBCC