cortex_var_63_c1: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory

[covux]

hey,

i am new to cortex_var and i am following the run_call.pl guide.

I have trouble getting cortex_var_63_c1 working.

I made "make NUM_COLS=1 MAXK=63 cortex_var"  in  /home/user/Downloads/CORTEX_release_v1.0.5.21

in the same place i used "bash install.sh" and "make cortex_var"

but i keep getting the error message: cortex_var_63_c1: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory


I use the following command: time cortex_var_63_c1 --kmer_size 61 --mem_height 16 --mem_width 2500 --pe_list R1_list,R2_list max_read_len 10000 --dump_binary ref.61.ctx --sample_id NAME


Do you have any tips how to resolve this problem?

Kind regards
Covux

[Zamin Iqbal]

Hi there

Exactly what version are you using? Does the problem go away with the tip of github?

https://github.com/iqbal-lab/cortex

regards

Zam

[covux]

hey,

I am using v1.05.21

what tip are you referring to?


Op maandag 15 mei 2017 15:30:57 UTC+2 schreef Zamin Iqbal:

[covux]

I got the solution.

I can't explain it very well.
a colleague gave me the solution.

for those that are more skilled in Linux read here: https://www.gnu.org/software/gsl/manual/html_node/Shared-Libraries.html


If you do

$ LD_LIBRARY_PATH=/usr/local/lib
$ export LD_LIBRARY_PATH

and afterwards run cortex_var the error message disappears and cortex_var starts running.

to make this a permanent solution you can also add the first command line in a bash script.

.bashrc  or .bash_profile

I hope this gives enough clues for people who encounter a similar problem. :)

covux

Op dinsdag 16 mei 2017 23:36:00 UTC+2 schreef covux: