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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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jellyfish 2 run error #22

Closed milw closed 10 years ago

milw commented 10 years ago

hi, I have installed jellyfish along with MaSuRCA, but am getting the following error from jellyfish-2.0:

scott@biolinux3:~/software/masurca/bin$ ./jellyfish-2.0 ./jellyfish-2.0: error while loading shared libraries: libjellyfish-2.0.so.2: cannot open shared object file: No such file or directory

The MaSuRCA install suggests that paths should be in the sr_example_configuration but there are no paths in that file... any suggestions?

gmarcais commented 10 years ago

Hi,

this is surprising. autoconf/automake is supposed to copy the path for the library in the executable. Did you move the directory containing the compiled software? What does 'chrpath jellyfish-2.0' returns?

Guillaume.

PS: You may have to install chrpath, but it should be available from all Linux package management system.

On Sun, Oct 5, 2014 at 2:57 PM, milw notifications@github.com wrote:

hi, I have installed jellyfish along with MaSuRCA, but am getting the following error from jellyfish-2.0:

scott@biolinux3:~/software/masurca/bin$ ./jellyfish-2.0 ./jellyfish-2.0: error while loading shared libraries: libjellyfish-2.0.so.2: cannot open shared object file: No such file or directory

The MaSuRCA install suggests that paths should be in the sr_example_configuration but there are no paths in that file... any suggestions?

  • echo creating sr_config_example.txt with correct PATHS creating sr_config_example.txt with correct PATHS
  • /home/scott/software/masurca/bin/masurca -g sr_config_example.txt

— Reply to this email directly or view it on GitHub https://github.com/gmarcais/Jellyfish/issues/22.

milw commented 10 years ago

hi Guillaume, it probably is because I tried to move something- the first compile attempt installed to the /usr/bin directory. I got it to work today by starting fresh from the tar archive and running the install script with DEST=/my/desired/location, so MaSuRCA is currently running (past the jellyfish stage already!) cheers- Scott