Camille Scott
Camille Scott
See https://github.com/dib-lab/dammit/projects/1.
shmlast preserves super long names; other programs truncate after the first space.
From some systems during DIBSI 2018: ``` TaskFailed - taskid:busco:trinity.nema.fasta-metazoa_odb9 busco:trinity.nema.fasta-metazoa_odb9 : Traceback (most recent call last): File "/home/dibtiger/miniconda3/envs/py3.dammit/bin/run_BUSCO.py", line 26, in from pipebricks.PipeLogger import PipeLogger ModuleNotFoundError: No module named...
The OSX version of TransDecoder fails when no features are found; this results in task failure, ending the dammit pipeline prematurely. This is a somewhat rare circumstance, and OSX is...
Current issues to resolve: - BUSCO requires python3. Get a side-by-side installation of it. - khmer requires GNU/4.8.3. The following programs do not have GNU/4.8.3 compatible modules installed: - BLAST+...
``` Traceback (most recent call last): File "/home/camille/miniconda/envs/bio/bin/dammit", line 4, in __import__('pkg_resources').run_script('dammit==0.0.7', 'dammit') File "/home/camille/miniconda/envs/bio/lib/python2.7/site-packages/pkg_resources/__init__.py", line 735, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/camille/miniconda/envs/bio/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1652, in run_script exec(code, namespace, namespace)...
WIP: Addresses #7. Currently supports weighted and unweighted adjacency matrices. For now, uses a seaborn heatmap. I've added a decorator for an optional dependency, and the function imports seaborn and...
During the brainstorming process we discussed supporting plots of summary statistics. Let's consider some possibilities... * degree distribution: like `plot_degree_dist(network, kde=False, ...)` * distribution of arbitrary node/edge attribute: `plot_node_attribute(network, 'weight',...