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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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can't load HTSLib Shared library despite it being on the $PATH; no config file to modify #1

Closed warrenmcg closed 9 years ago

warrenmcg commented 9 years ago

Hi,

I'm excited to use your tool on some of my data. However, I have an error that I can't figure out how to solve.

Here is the output I see:

$ ./giremi
giremi: error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory

However, my $PATH variable includes the location of this file:

$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/lib
$ ls /usr/local/lib/libhts.so.1
/usr/local/lib/libhtso.so.1

Your README.md says Please make sure your dynamic library path in your configuration file includes the directory in which HTSlib is installed, but I don't see what configuration file I'm supposed to be modifying, and I don't know how to recompile the giremi script from source.

Let me know how I can solve this issue.

Thanks, Warren

zhqingit commented 9 years ago

Hi Warren,

The library directory should be included in this variable: $LD_LIBRARY_PATH not the $PATH.

Let me know if you have other questions.

Best, Qing

2015-09-03 18:10 GMT-07:00 Warren McGee notifications@github.com:

Hi,

I'm excited to use your tool on some of my data. However, I have an error that I can't figure out how to solve.

Here is the output I see:

$ ./giremi giremi: error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory

However, my $PATH variable includes the location of this file:

$ echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/lib $ ls /usr/local/lib/libhts.so.1 /usr/local/lib/libhtso.so.1

Your README.md says Please make sure your dynamic library path in your configuration file includes the directory in which HTSlib is installed, but I don't see what configuration file I'm supposed to be modifying, and I don't know how to recompile the giremi script from source.

Let me know how I can solve this issue.

Thanks, Warren

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/1.

warrenmcg commented 9 years ago

That worked! Thank you! You should probably update your installation instructions to let users know that $LD_LIBRARY_PATH is the variable that needs to be set.

zhqingit commented 9 years ago

Thanks, Warren.

Best, Qing

2015-09-04 9:09 GMT-07:00 Warren McGee notifications@github.com:

That worked! Thank you! You should probably update your installation instructions to let users know that $LD_LIBRARY_PATH is the variable that needs to be set.

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/1#issuecomment-137778787.