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install libatlas3 without sudo / root access

I am trying to run rMATS Turbo on a CentOS linux cluster. My runs are generating the following error...

rMATSexe: error while loading shared libraries: libblas.so.3: cannot open shared object file: No such file or directory

The cluster system does not give me root access so I can't use the typical sudo apt-get install libatlas3-base install method that people commonly suggest online. Does anyone know where I can find this package to install it manually? Or alternatively is there another package that contains this that i can install using anaconda conda install?

rmats libatlas3 install conda rna-seq
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updated by Biostar Biostar • written by paulranum11 paulranum11

It looks like rMATS from bioconda is the slow version rmats: 3.2.5-py27h24bf2e0_2

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written by paulranum11 paulranum11

I'm not familiar with rMATS, so also not with a slow or fast version. If the version on bioconda is outdated (I guess that is what you mean) then we have to update the recipe.

For reference, there is already a pull request to update this, but some issues had to be sorted out. We'll see what we can do.

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written by WouterDeCoster WouterDeCoster

There are currently license issues with rMATs that need to be cleared up before it can be distributed by bioconda. You can follow the discussion about that here.

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written by Devon Ryan Devon Ryan

Try installing openblas in conda and exporting that path as LD_LIBRARY_PATH.

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written by Devon Ryan Devon Ryan

Thanks for this suggestion! I installed openblas using conda but how do I export the path as LD_LIBRARY_PATH?

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written by paulranum11 paulranum11

export LD_LIBRARY_PATH=/the/path/to/the/directory/with/the/blas/library.

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written by Devon Ryan Devon Ryan

Sorry to make this so tedious... I am having the hardest time figuring out where the openblas library is stored in anaconda. I was able to locate some openblas files using find ~/anaconda3/ -iname "*openblas*". However it is not clear to me which is the blas library that I need.

    ./pkgs/openblas-0.3.3-ha44fe06_1
./pkgs/openblas-0.3.3-ha44fe06_1/include/openblas_config.h
./pkgs/openblas-0.3.3-ha44fe06_1/lib/libopenblasp-r0.3.3.a
./pkgs/openblas-0.3.3-ha44fe06_1/lib/libopenblas.a
./pkgs/openblas-0.3.3-ha44fe06_1/lib/libopenblas.so.0
./pkgs/openblas-0.3.3-ha44fe06_1/lib/pkgconfig/openblas.pc
./pkgs/openblas-0.3.3-ha44fe06_1/lib/cmake/openblas
./pkgs/openblas-0.3.3-ha44fe06_1/lib/cmake/openblas/OpenBLASConfigVersion.cmake
./pkgs/openblas-0.3.3-ha44fe06_1/lib/cmake/openblas/OpenBLASConfig.cmake
./pkgs/openblas-0.3.3-ha44fe06_1/lib/libopenblas.so
./pkgs/openblas-0.3.3-ha44fe06_1/lib/libopenblasp-r0.3.3.so
./pkgs/blas-1.0-openblas.tar.bz2
./envs/python2/include/openblas_config.h
./envs/python2/conda-meta/libopenblas-0.3.3-h5a2b251_3.json
./envs/python2/conda-meta/blas-1.0-openblas.json
./envs/python2/conda-meta/openblas-devel-0.3.3-3.json
./envs/python2/conda-meta/openblas-0.3.3-ha44fe06_1.json
./envs/python2/lib/libopenblas.so
./envs/python2/lib/libopenblasp-r0.3.3.so
./envs/python2/lib/libopenblas.so.0
./envs/python2/lib/pkgconfig/openblas.pc
./envs/python2/lib/libopenblas.a
./envs/python2/lib/libopenblasp-r0.3.3.a
./envs/python2/lib/cmake/openblas
./envs/python2/lib/cmake/openblas/OpenBLASConfig.cmake
./envs/python2/lib/cmake/openblas/OpenBLASConfigVersion.cmake

Am i looking for libblas.so.3?

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written by paulranum11 paulranum11

Look for libblas.so, which will be under ./pkgs/openblas-0.3.3-ha44fe06_1/lib/. Whether that's ABI compatible remains to be seen, regardless you might need to create a symlink to it called libblas.so.3 so it's picked up.

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written by Devon Ryan Devon Ryan

I found the libblas.so library and linked it using the following command.

ln -s ~/anaconda3/pkgs/openblas-0.3.3-ha44fe06_1/lib/libblas.so ~/anaconda3/lib/libblas.so.3

However, I am still getting the same error. Is ~/anaconda3/lib the correct location to use to make this shared library availible? Do i need to use any additional commands to rebuild the index of libraries or anything?

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written by paulranum11 paulranum11

No, that should suffice, it looks like they build against something that isn't ABI compatible (so it goes).

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written by Devon Ryan Devon Ryan

The cluster system does not give me root access so I can't use the typical sudo apt-get install libatlas3-base

Clusters in general have administrators, ask them to install libblas. It is possible it is already installed at a non-standard location, if so, they will tell you where and how to use it.

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written by h.mon h.mon

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