Boost library error, running Tophat

[Aholton]

Been fighting with Tophat installation and finally got everything setup (I think). Then I get an error about Boost (which I had the most problems with due to permissions being denied). This is the error I get at the end of the run

Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.50.0: cannot open shared object file: No such file or directory

Not sure what I need to move from the Boost libraries. Was hoping ya'll could help me out a bit.

Thanks!

[alec]

Either that file does not exist or it is not on your library search path. Assuming it exists (it will normally be in boost/lib), the easiest way to change your library search path is:

LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH

[Aholton]

Thanks for the quick response, I have Tophat, Boost, bowtie2, and samtools all located within my /usr/local folder, i installed them all from there and have all the libraries set to default (/usr/local/bin or /usr/local/lib)

I entered the command you typed to re assert that the libraries were in /usr/local/lib. I even went into the folder (/usr/local/lib) and saw that it had numerous libboost files in it.

I don't know if it was an error on the boost libraries fault or if Tophat can't find the libraries cause of a Tophat installation error

[alec]

I think you need to do "export LD_LIBRARY_PATH" as well to make it visible to tophat

[Aholton]

Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.50.0: cannot open shared object file: No such file or directory

I tried to use your new command and it still came up with that error. I know in the lib folder there is that libboost_thread.so.1.50.0 file. I just don't know why it's acting up all the sudden.

[Aholton]

Nevermind everyone! The export command worked, I was really exhausted when I tried to fix one of the servers using the export command but I was using it in the wrong server (silly me). Thank you for your quick response time.

Hopefully soon I'll be making some guides based on my experiences with doing Bioinformatics so that the field can grow and attract more attention from undergrads looking to specialize.

[owwa]

Hi Aholton,

I encountered the same error. Could you please share your detailed way to solve this? Thank.

[owwa]

I do "export PATH=$PATH:/usr/local/lib", but it don't work.

The file "libboost_thread.so.1.50.0" is also located in /usr/local/lib for me.

[Aholton]

LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH

Try typing that command, the "/path/to/boost/lib" for you would be "/usr/local/lib". The only other thing I can think that I did differently was release some of the permissions on the files because Boost was messing up. By that I mean that I changed permissions to read and write for all boost related files (either done through a GUI ftp service or through the command chmod ug+rwx <name_of_file>.

[owwa]

LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH

Try typing that command, the "/path/to/boost/lib" for you would be "/usr/local/lib". The only other thing I can think that I did differently was release some of the permissions on the files because Boost was messing up. By that I mean that I changed permissions to read and write for all boost related files (either done through a GUI ftp service or through the command chmod ug+rwx <name_of_file>.

Many thanks! Aholton

but the problem is still here. Actually, i don't know what "all boost related files" are. Could you please tell me the exact files or files folder?

[owwa]

The error showed that libboost_thread.so.1.50.0: cannot open shared object file, I also don't know what the "shared object file" is.

[Aholton]

That means it's still not recognizing it, sorry it took so long to respond. Had to make an emergency trip to CDC.

All boost related files are all the files within the Boost folder with all the files in it (including the libraries".lib files"). I had some problems with permissions the first time I did it.

Did you run boostrap.sh or did you simply run bjam?

[owwa]

Many thanks! I'm a newer for tophat, just need the boost library files, I think I just symply run bjam. The error had dispeared, I had some problems with permissions too. Thank you again...

[Aholton]

No problem! If you need anything else feel free to private message me

[super0925]

LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH

Try typing that command, the "/path/to/boost/lib" for you would be "/usr/local/lib". The only other thing I can think that I did differently was release some of the permissions on the files because Boost was messing up. By that I mean that I changed permissions to read and write for all boost related files (either done through a GUI ftp service or through the command chmod ug+rwx <name_of_file>.

Hi How do you solve the error?
I type "LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH" but it still get the error. And meanwhile I have got the output, e.g. accepted_hits.bam and the align_summart.txt, are they reliable?