Question: install libatlas3 without sudo / root access
0
gravatar for paulranum11
4 months ago by
paulranum1130
paulranum1130 wrote:

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?

ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 4 months ago by paulranum1130

Have you installed rMATS through bioconda?

ADD REPLYlink written 4 months ago by WouterDeCoster37k

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...

ADD REPLYlink modified 4 months ago • written 4 months ago by paulranum1130

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

ADD REPLYlink written 4 months ago by paulranum1130
1

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 If the version on bioconda is outdated (I guess that is what you mean) then we have to update the recipe.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

ADD REPLYlink modified 4 months ago • written 4 months ago by WouterDeCoster37k

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.

ADD REPLYlink written 4 months ago by Devon Ryan88k

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

ADD REPLYlink written 4 months ago by Devon Ryan88k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by paulranum1130

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

ADD REPLYlink written 4 months ago by Devon Ryan88k

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?

ADD REPLYlink modified 4 months ago • written 4 months ago by paulranum1130

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.

ADD REPLYlink written 4 months ago by Devon Ryan88k

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?

ADD REPLYlink modified 4 months ago • written 4 months ago by paulranum1130

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

ADD REPLYlink written 4 months ago by Devon Ryan88k

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.

ADD REPLYlink written 11 weeks ago by h.mon24k
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