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could not load: libhts.so, but in LD_LIBRARY_PATH #1
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you need to do: not just set it. |
That's what I did, more specifically, I added the following line in my ~/.bashrc (and sourced the file afterwards)
Trying again, explicitly as you suggested:
|
what does |
The libhts.so files turn out to link to
Does that look as expected? Should I try installing htslib without conda? |
yes. I would try that. it's easy enough to build and then you just set LD_LIBRARY_PATH to the directory. |
Thanks, that seems to do the trick:
Would there be an "easy" way to solve the outdated libc.so.6 issue on the other server? If not I'll have to talk to our sysadmin about fixing mounts etc to give me access to the data on the recent server... To be more specific, this is the error on the older server:
|
so your troubles have highlighted the need for a binary for older systems. I am also fixing some severe (but shallow) bugs. How about you wait until next week and I'll make a binary for the older systems as well. I'd rather you use it successfully and report on substantial issues/features rather than test your patience with annoying issues like these. |
That sounds great. |
sorry for the delay. See my response here: #4 (comment) I'll be working on indelope again this week and hope to make good progress on accuracy and then I'll work on improving distribution/install. |
Thanks for the update, I'll keep an eye on this repository. |
Hi,
I tried to install libhts.so manually and set the LD_LIBRARY_PATH for all found libhts.so seperately, however, it didn't work.
ex.
Is there any else method to solve it? Thanks in advance. Sincerely, |
Hmm. Are you sure that libhts.so is still there? What does |
Hi,
My usual CentOS6 server has an outdated libc.so.6 so I have to use a more recent OS. Sysadmin told me this cannot be updated, unfortunately. Anyway, on the other server (CentOS7) I downloaded the binary and installed the libhts.so using
conda install htslib
.Since
find ~ -name libhts.so
returnsI changed the LD_LIBRARY_PATH to
/home/wdecoster/anaconda3/lib/:/home/wdecoster/anaconda3/pkgs/htslib-1.6-0/lib/
Yet, when executing
./indelope -h
I get:Did I mess up somewhere?
I can install nim and try compiling with the suggested -d:nimDebugDlOpen flag, or what do you suggest?
Installation on my Ubuntu17.10 desktop does work.
Cheers,
Wouter
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