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Repo to track issues with TSD as tickets
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Problems installing LD SCore #32

Closed E-Claire closed 4 years ago

E-Claire commented 4 years ago

After loading Anaconda and Python 2.7 I get the below error message. (The screenshot is from p471 but I get the same message on p697). ldsc_issue

ofrei commented 4 years ago

@E-Claire Hi there. For sure we need to find an easy way of running ldsc on TSD. I've tried using " Anaconda3/5.3.0" only, i.e. without "module load ptyhon2.gnu/2.7.3". Generally, Anaconda contains python, and Anaconda3 can manage python2 environments. However, the problem is that Anaconda tries to reach internet for installing modules - that obviously don't work on TSD. We can check with TSD if they have a mirror for Anaconda.

Another option is to try 

module load python2.gnu/2.7.15
pip install --user cython
pip install --user --index-url=https://pypi.tsd.usit.no/simple bitarray==0.8 nose==1.3  pybedtools==0.7  scipy==0.18  pandas==0.20 numpy==1.12

Could you please try this and let me know if it worked?

ofrei commented 4 years ago

Installation-wise it worked for me, but I haven't tried to run ldsc in that environment: image

ofrei commented 4 years ago

@E-Claire Good to know this is now working!

To activate the conda environment, run: source /cluster/projects/p471/ldsc-activation, substituting p471 for p697 in the command when logged on to p697.

To deactivate run: source deactivate.