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Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
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How to run binary file? #2

Closed sjm0240111 closed 4 years ago

sjm0240111 commented 4 years ago

Hello, I don't know how to run the binary file, could anyone give a bit hint? I've failed running it by simply typing ./taiji-Linux-x86_64, which I think is the binary file.

kaizhang commented 4 years ago

@sjm0240111 You need to give the "execute" permission to the file first: chmod +x taiji-Linux-x86_64

sjm0240111 commented 4 years ago

Yes, I did try that, only to find the error Segmentation fault :

(base) -bash-4.2$ ll | grep taiji -rwxr-xr-x. 1 exer3 exer3 28180480 Jan 22 04:55 taiji-Linux-x86_64 (base) -bash-4.2$ ./taiji-Linux-x86_64 Segmentation fault

kaizhang commented 4 years ago

Sorry for the late response. What's the version of the taiji and Linux system you were using?

sjm0240111 commented 4 years ago

Sorry for my late response too! I'm using the latest v1.1.0.I will try to compile the source first, but the question is that I'm not the root user.

kaizhang commented 4 years ago

You don't need to have root to compile the program. If you can tell me your OS information, I can try to find out why the binary doesn't work on your platform.

sjm0240111 commented 4 years ago

I'm not sure if this information is right. (base) -bash-4.2$ cat /etc/redhat-release CentOS Linux release 7.6.1810 (Core) (base) -bash-4.2$ cat /proc/version Linux version 3.10.0-957.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) )

kaizhang commented 4 years ago

It looks like you are using CentOS 7. The binary was compiled on CentOS 7 so that should work unless your system was recently upgraded.

What is the output of ldd taiji-Linux-x86_64?

If you want to compile from source, you can follow the instructions here: https://taiji-pipeline.github.io/documentation/install.html.

You don't need the root privilege but the compilation will take a while (1~2 hours).

sjm0240111 commented 4 years ago

When I run ldd taiji-Linux-x86_64 it says not a dynamic executable. If I compile from source, I had to install stack first, which now requires root privilege, I will try installing it.

kaizhang commented 4 years ago

I see. Then you must have downloaded the wrong version. Please use this link to download the correct version: https://github.com/Taiji-pipeline/Taiji/releases/download/v1.1.0/taiji-Linux-x86_64

The binary should be dynamically linked. And the stack does not need root. You can download the stack binary and just run it.

sjm0240111 commented 4 years ago

Yeah! I downloaded your correct file, which is bigger than my previous one. I guess last time I met some transfer error. It works pretty well after installing igraph library. Thanks a lot!