Question: Emboss Shared Libraries
2
gravatar for Daniel Standage
10.0 years ago by
Daniel Standage4.0k
Davis, California, USA
Daniel Standage4.0k wrote:

I installed EMBOSS yesterday on a system running Ubuntu. I did the canonical './configure; make; sudo make install' and I didn't see any errors. However, today I ran getorf and got the following error.

/usr/local/bin//getorf: error while loading shared libraries: libacd.so.6: cannot open shared object file: No such file or directory

I checked, and there is a copy of this file both in $installDir/ajax/acd/.libs/ and /usr/local/lib. Indeed, when I linked /usr/local/lib/libacd.so.6 to /usr/lib/libacd.so.6, it did not complain about this library any more--it complained about another one! How do the binaries know where to find the libraries? Is there some configuration or environmental variable I am not setting correctly?

I know that this question might be general to Linux/Unix, but I hope it's specific enough to EMBOSS to bring up in this community.

linux • 2.8k views
ADD COMMENTlink written 10.0 years ago by Daniel Standage4.0k
8
gravatar for biobot 0.0.77.a.1099
10.0 years ago by
UK
biobot 0.0.77.a.10996.1k wrote:

Check that ldconfig has been run and is configured to include /usr/local/lib in its search path. The relevant config file is /etc/ld.so.conf (or similar). E.g. mine contains

/usr/local/lib
/usr/X11R6/lib

Then run

sudo ldconfig

You should never need to twiddle with LD_LIBRARY_PATH directly.

ADD COMMENTlink modified 15 months ago by _r_am31k • written 10.0 years ago by biobot 0.0.77.a.10996.1k

Thanks for the explanation of ldconfig!

ADD REPLYlink written 10.0 years ago by Daniel Standage4.0k

Will the wonders ever cease ... I have been twiddling with the LD_LIBRARY_PATH for a decade or more ... somehow I never read about ldconfig

ADD REPLYlink modified 15 months ago by _r_am31k • written 10.0 years ago by Istvan Albert ♦♦ 85k
3
gravatar for brentp
10.0 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

Often on ubuntu linux you can solve this type of problem by running:

$ sudo ldconfig

that updates the links for the linker.

ADD COMMENTlink modified 15 months ago by _r_am31k • written 10.0 years ago by brentp23k
2
gravatar for Pierre Lindenbaum
10.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

How do the binaries know where to find the libraries? Is there some configuration or environmental variable I am not setting correctly?

The path to the dynamic libraries is usually stored in the variable $LD_LIBRARY_PATH

ADD COMMENTlink modified 15 months ago by _r_am31k • written 10.0 years ago by Pierre Lindenbaum131k

I've read a lot recently saying that the $LD_LIBRARY_PATH variable is not a good long term solution, but was designed for testing new libraries. A lot of people cite problems when permanently adding non-default libraries to $LD_LIBRARY_CONFIG. Was EMBOSS designed to rely on this environmental variable?

ADD REPLYlink modified 15 months ago by _r_am31k • written 10.0 years ago by Daniel Standage4.0k

No, as explained in the accepted answer EMBOSS installs to /usr/local/lib, you just have to use ldconfig to add that path because it's not the Ubuntu default.

ADD REPLYlink written 10.0 years ago by Neilfws49k
1
gravatar for D. Puthier
10.0 years ago by
D. Puthier330
France/Marseille/Inserm
D. Puthier330 wrote:

If you are running ubuntu you should try to install EMBOSS through apt-get.

sudo apt-get install emboss-data emboss-doc embassy-domainatrix embassy-domalign
ADD COMMENTlink modified 15 months ago by _r_am31k • written 10.0 years ago by D. Puthier330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1508 users visited in the last hour