Abhishek Sarkar
Abhishek Sarkar
Our cluster is configured to use consumable resources with different names for hard memory limits, GPUs, etc. Requesting these resources requires writing to the native specification property of the Job...
I'm manually starting a remote kernel on a compute cluster, then connecting my ipython source blocks to it using a named session. ``` #+BEGIN_SRC ipython :session kernel-aksarkar.json :async t :results...
Add test cases for Poisson-uniform mixture likelihood computations Compute marginal PMF over a point mass using dpois directly This fixes issue #114
On simulated NB data (https://users.rcc.uchicago.edu/~aksarkar/pois-mode-est.Rds), fitting with log link gets a much worse log likelihood than with identity link. ``` > dat with(dat, summary(MASS::glm.nb(x ~ offset(log(s))))$twologlik / 2) [1] -2008.504...
The pipeline checks that the input bam file is indexed by checking for the `.bai` extension, which means that indexes `.csi` are not allowed (although they should be). https://github.com/caleblareau/bap/blob/44061cdcc16d60d6a757d518d55b4dfe66afb436/bap/cli_bap2.py#L145-L146
https://github.com/caleblareau/bap/blob/44061cdcc16d60d6a757d518d55b4dfe66afb436/setup.py#L7 This lead to a missing dependency in our internally built conda package metadata that wasn't discovered until runtime.
After running the fragment in the README ``` conda install -c conda-forge -c bioconda r-cellassign ``` I expect that all required packages are installed. However, I need to additionally run...
We typically run Batch workflows on AWS spot instances to take advantage of cost savings when possible. However, when some redun task is interrupted due to its host being terminated,...