Issue running RepeatDetector

[MaestSi]

Dear all, I tried running the executable in RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/bin/RepeatDetector. However, when running ./RepeatDetector --help I got this error: ./RepeatDetector: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory I tried setting variable LD_LIBRARY_PATH to RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/lib, but that didn't solve the issue. I also tried running RepeatDetector from the available singularity image, with:

(base) -bash-4.2$ singularity run repeat_detector.sif /bin/bash
Apptainer> RepeatDetecter --help
RepeatDetecter: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

However, I noticed only RepeatDetecter executable was available in the image (with 'e', but this might just be a typo) and a similar error appeared. How can I solve this issue? Thanks in advance, Simone

[MaestSi]

Hi, I think I found a temporary fix for the issue. In order to solve the issue for the executable version, I created a symbolic link to libhts.so with name libhts.so.2 with command:

cd ./RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/lib
ln -s libhts.so libhts.so.2

This was enough to see the help message when typing RepeatDetector --help, so it should be working now. While, since the singularity image was complaining of not being able to find libhts.so.3, and being the system read-only, I created also a link to libhts.so named libhts.so.3 in the same lib directory with command: ln -s libhts.so libhts.so.3 Then, I executed the singularity image in interactive mode, mounting also some host directories, with: singularity run --bind /lustre/home:/lustre/home repeat_detector.sif /bin/bash And then I added the path of folder containing libhts.so.3 to LD_LIBRARY_PATH with: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/lustrehome/path/to/RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/lib Now, also RepeatDetecter --help shows the help message with no further errors. If you think these are reasonable fixes, you may consider adding the symbolic links in the lib folders of both the Linux executable and the singularity image. Best, SM

[DionLab]

Dear Simone Many thanks for your messages. Our Bioinformatician, Ruban, is on annual leave and will get back to you on his return. Best Vincent

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From: Simone Maestri @.> Sent: 21 October 2024 8:47 AM To: DionLab/RepeatDetector @.> Cc: Subscribed @.***> Subject: Re: [DionLab/RepeatDetector] Issue running RepeatDetector (Issue #5)

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

Hi, I think I found a temporary fix for the issue. In order to solve the issue for the executable version, I created a symbolic link to libhts.so with name libhts.so.2 with command:

cd ./RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/lib ln -s libhts.so libhts.so.2

This was enough to see the help message when typing RepeatDetector --help, so it should be working now. While, since the singularity image was complaining of not being able to find libhts.so.3, and being the system read-only, I created also a link to libhts.so named libhts.so.3 in the same lib directory with command: ln -s libhts.so libhts.so.3 Then, I executed the singularity image in interactive mode, mounting also some host directories, with: singularity run --bind /lustre/home:/lustre/home repeat_detector.sif /bin/bash And then I added the path of folder containing libhts.so.3 to LD_LIBRARY_PATH with: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/lustrehome/path/to/RepeatDetector/RepeatDetector-1.0.15eb445-Release-Linux-x86_64/lib Now, also RepeatDetecter --help shows the help message with no further errors. If you think these are reasonable fixes, you may consider adding the symbolic links in the lib folders of both the Linux executable and the singularity image. Best, SM

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