install libatlas3 without sudo / root access

Question

[paulranum11]

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?

[WouterDeCoster]

Have you installed rMATS through bioconda?

[paulranum11]

No I installed rMATS from here http://rnaseq-mats.sourceforge.net/rmats4.0.1/

Do you know if rMATS from bioconda is the 4.0.1 + version with the speed increase "rMATS Turbo"? I will try to check and find out...

[paulranum11]

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

[WouterDeCoster]

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 If the version on bioconda is outdated (I guess that is what you mean) then we have to update the recipe.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.

[Devon Ryan]

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.

[Devon Ryan]

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

[paulranum11]

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

[Devon Ryan]

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

[paulranum11]

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?

[Devon Ryan]

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.

[paulranum11]

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?

[Devon Ryan]

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

[h.mon]

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.