SeCaPr - Sequence Capture Processor

The-Bioinformatics-Group / Albiorix

Code used for configuration and administration of the bioinformatics computer cluster Albiorix at the Department of Biological and Environmental Sciences and Marine sciences, University of Gothenburg.

http://albiorix.bioenv.gu.se/

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SeCaPr - Sequence Capture Processor #101

Closed RominaSSBatista closed 6 years ago

RominaSSBatista commented 7 years ago

It seems the updates @tobiashofmann88 made is not available yet. Can we have it, @mtop ? SeqCaPr. I would like to know if it is straightforward activate the environment by source activate cmmd line on Albiorix? thanks!!!

mtop commented 7 years ago

Hi @RominaSSBatista The latest version of Tobis code is now available under Anaconda v4.4.0 module load Anaconda2/v4.4.0.

RominaSSBatista commented 7 years ago

Hi @mtop I am trying to use it by typing:

$ module load Anaconda2/v4.4.0 $ secapr --help

I get the following msg: Traceback (most recent call last): File "/usr/local/packages/anaconda2-4.4.0/bin/secapr", line 6, in <module> from pkg_resources import load_entry_point File "/usr/local/packages/anaconda2/lib/python2.7/site-packages/pkg_resources.py", line 2850, in <module> working_set.require(__requires__) File "/usr/local/packages/anaconda2/lib/python2.7/site-packages/pkg_resources.py", line 696, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/local/packages/anaconda2/lib/python2.7/site-packages/pkg_resources.py", line 594, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: secapr==1.0.2
I am wondering if you did this command? conda create -n secapr_env -c bioconda secapr
Because I am not been able to source activate secapr_env as Tobi suggests in his code.

thanks! 👍

tandermann commented 7 years ago

in case you want to install secapr locally on your Albiorix home directory you can also just type the following: sh /usr/local/ubin/envs/install_and_activate_secapr.sh

Then you can activate the environment like this:

source ./miniconda/bin/activate secapr

Best, Tobi

mtop commented 7 years ago

I've made a global installation now. source activate secapr_envworks now.

tandermann commented 7 years ago

thats great news, then I don't have to have all students install the software locally! Thanks Mats!

RominaSSBatista commented 7 years ago

I was wondering to do it in my home directory after @mtop ask to clean it because it is getting full... But I just made it... I will remove and use the global one that mats installed. Thanks tobi & Mats!!!!

tandermann commented 7 years ago

also be aware that you'll have to reactivate the secapr_env if you qlogin or run an sge script on high_mem or node0 (simply add source activate secapr_env to the sge script)

RominaSSBatista commented 7 years ago

ok! thanks tobi!