No libssw.so after executing 'make' in the src folder

[mcolic]

Hi,

After I execute 'make' in the src folder there is no libssw.so file that needs to be copied into my program. I have also tried gcc compiling: gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h - but gives me a clang error: clang: error: cannot specify -o when generating multiple output files! Can you please assist with this?

Thank you.

[mengyao]

Please run ‘make default’.

Yours,

Mengyao

On Apr 11, 2022, at 6:00 PM, Medina Colic @.***> wrote:

Hi,

After I execute 'make' in the src folder there is no libssw.so file that needs to be copied into my program. I have also tried gcc compiling: gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h - but gives me a clang error: clang: error: cannot specify -o when generating multiple output files! Can you please assist with this?

Thank you.

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[mcolic]

Hi Mengyao,

Thank you for a quick response. When I do run the make default I do get both libssw.so and ssw_lib.py, but when I need to use the module it tells me that it's an incompatible architecture (have 'arm64', need 'x86_64'). I should specify that I am running this on MacBook with M1 chip. Thank you. Best, Medina

[mengyao]

Hi Medina,

Arm64 is for MacBook M1 chip, while x86_64 is for Intel CPUs.

When you compile SSW on your MacBook, it will generate the libssw.so for arm64.

Your error looks like your python program expects a x86_64 libssw.so. I suggest you compile SSW on a linux machine. The libssw.so will be for x86_64.

I will try to make a new release that have compiled binary files for different systems soon.

Bests,

Mengyao

On Apr 14, 2022, at 2:31 PM, Medina Colic @.***> wrote:

Hi Mengyao,

Thank you for a quick response. When I do run the make default I do get both libssw.so and ssw_lib.py, but when I need to use the module it tells me that it's an incompatible architecture (have 'arm64', need 'x86_64'). I should specify that I am running this on MacBook with M1 chip. Thank you. Best, Medina

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[mcolic]

Hi Mengyao,

I have switched to an Intel MacBook. I installed the library with 'make default', and have both files libssw.so and ssw_lib.py. However, I am trying to use the library within another package tuba-seq (https://github.com/petrov-lab/tuba-seq), and when I use the scripts that are dependent on the libssw.so, I keep getting the error saying: "libssw.so does not exist in PATH" - which comes from one of the scripts in the tuba-seq package. I am not sure how to resolve this error. Can you please provide any assistance or suggestions?

Thanks, Medina

[mengyao]

According to the error message, I think you just need to add the libssw.so path into your PATH viable. You may need to add export PATH=:PATH in your .bashrc file.

Mengyao

Sent from my iPhone

On Apr 20, 2022, at 10:38, Medina Colic @.***> wrote:

 Hi Mengyao,

I have switched to an Intel MacBook. I installed the library with 'make default', and have both files libssw.so and ssw_lib.py. However, I am trying to use the library within another package tuba-seq (https://github.com/petrov-lab/tuba-seq), and when I use the scripts that are dependent on the libssw.so, I keep getting the error saying: "libssw.so does not exist in PATH" - which comes from one of the scripts in the tuba-seq package. I am not sure how to resolve this error. Can you please provide any assistance or suggestions?

Thanks, Medina

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