razrichter / grid_scripts Goto Github PK
View Code? Open in Web Editor NEWScripts for working on SGE grids
Scripts for working on SGE grids
The qrun version I'm using is the current one on the GitHub from 2019.07.03
I'm not able to access the PATH in my conda environment. Though, it is recognizing my conda environment. Demonstrations below:
-bash-4.1$ source activate star_env
(star_env) -bash-4.1$ which python
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/star_env/bin/python
(star_env) -bash-4.1$ source activate star_env
(star_env) -bash-4.1$ echo $CONDA_PREFIX
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/star_env
(star_env) -bash-4.1$ cat manifest.tsv | qrun -P 0749 -N qrun_test -c "source activate star_env; which python; which conda; which STAR; echo $CONDA_PREFIX; echo {1}; echo {2}"
cat: manifest.tsv: No such file or directory
removed environment variable LD_LIBRARY_PATH from submit environment - it is considered a security issue
Your job 10251883 ("qrun_test") has been submitted
(star_env) -bash-4.1$ cat qrun_test.o10251883
/usr/local/bin/python
/usr/local/devel/ANNOTATION/jespinoz/anaconda/condabin/conda
/usr/local/bin/STAR
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/star_env
{1}
{2}
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