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Gossamer bioinformatics suite
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Gossamer installation [file INSTALL cannot copy file] #27

Closed sushang-thu closed 4 years ago

sushang-thu commented 4 years ago

Hi,

I ran into an error when installing gossamer onto Ubuntu. It showed in the

" make install " step

CMake Error at src/cmake_install.cmake:47 (file): file INSTALL cannot copy file "/home/shang/gossamer/build/src/goss" to "/usr/local/bin/goss". Call Stack (most recent call first): cmake_install.cmake:42 (include) Makefile:128: recipe for target 'install' failed make: *** [install] Error 1

any suggestions? I am running a WSL Ubuntu on Windows 10. I first installed all the recommended prerequisites and then git clone gossamer.

cd gossamer mkdir build cd build cmake .. make make test make install

Thanks very much!

beyondpie commented 4 years ago

@sushang-thu if you solve this issue, you could close it.

Deguerre commented 4 years ago

You may be the first to try to build Gossamer on WSL, so thanks for trying it out!

I'm not very familiar with WSL, but my first impression is that either /usr/local/bin doesn't exist, or the permissions are not set correctly.

Can you try sudo make install instead of make install?

beyondpie commented 4 years ago

Hi, @Deguerre

Shang has installed the program. and we just don't move the program to that dir, which might need a root dir (we haven't tested the existence of /usr/local/bin).

Since most of the users would install the program without root permission, it might be better if you can support the non-root version of this program. According to our experience, not using sudo and just simply following your cmakefile is enough (except the movement of the executable file finally to /usr/local/bin).

Thank you very much for your work!

Songpeng

sushang-thu commented 4 years ago

Thanks all,

I am now running the xenome index command on WSL (Ubuntu). After several hours, 23 idx files were created but it seems that the command is still running. image

I will close this issue anyway.

Deguerre commented 4 years ago

Thanks for this. Two comments:

  1. You can install xenome in a different directory telling CMake where to install:

cmake -DCMAKE_INSTALL_PREFIX=~/.local/or/wherever/you/want etc etc

  1. There is an outstanding bug in the released version of xenome that under some circumstances there's an infinite loop in index generation. You can try -T 1 (IIRC, -T 8 still works fine for queries, just not index generation).