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sreeramkannan / Shannon

RNA-Seq
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Mention SuiteSparse in installation instructions #16

Open standage opened 7 years ago

standage commented 7 years ago

Hi Sreeram,

I failed to get Shannon to install on two different HPC environments (BLAS/LAPACK issues), and finally gave up and tried AWS. All of the Ubuntu apt-get instructions work, but the pip install cvxopt did not work without installing an additional prerequisite: SuiteSparse. This is listed as a new dependency in the CVXOPT documentation, but many people will not go as far to read their documentation since you provide the pip and apt-get install commands in Shannon's installation instructions.

It should be trivial to add sudo apt-get install libsuitesparse-dev to the instructions, and could save a lot of headache down the road.

Thanks!

sreeramkannan commented 7 years ago

Hi, Thanks a lot for trying out Shannon and for the inputs. I will add this to the docs.

Best Sreeram

On Mon, Jan 16, 2017 at 2:33 AM, Daniel Standage notifications@github.com wrote:

Hi Sreeram,

I failed to get Shannon to install on two different HPC environments (BLAS/LAPACK issues), and finally gave up and tried AWS. All of the Ubuntu apt-get instructions work, but the pip install cvxopt did not work without installing an additional prerequisite: SuiteSparse. This is listed as a new dependency in the CVXOPT documentation, but many people will not go as far to read their documentation since you provide the pip and apt-get install commands in Shannon's installation instructions.

It should be trivial to add sudo apt-get install libsuitesparse-dev to the instructions, and could save a lot of headache down the road.

Thanks!

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standage commented 7 years ago

Software is hard! :(

My first successful install was on an Ubuntu system, but ran into trouble with CVXOPT again when installing on a Fedora system. Per https://github.com/cvxopt/cvxopt/issues/77, after installing SuiteSparse dnf install suitesparse-devel I had to set export CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse before CVXOPT would install properly.

sreeramkannan commented 7 years ago

Thanks again Daniel for your inputs. I really appreciate your posting them here for the entire user group.

On Tue, Jan 17, 2017 at 10:21 AM, Daniel Standage notifications@github.com wrote:

Software is hard! :(

My first successful install was on an Ubuntu system, but ran into trouble with CVXOPT again when installing on a Fedora system. Per cvxopt/cvxopt#77 https://github.com/cvxopt/cvxopt/issues/77, after installing SuiteSparse dnf install suitesparse-devel I had to set export CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse before CVXOPT would install properly.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sreeramkannan/Shannon/issues/16#issuecomment-273253479, or mute the thread https://github.com/notifications/unsubscribe-auth/ANm234JUV0K9fmnbiJFLDl471X83SHc0ks5rTQaugaJpZM4LkZqK .