Michael's Questions

[kwkroll32]

Do we need gene name lists in the config file?
If you are not installing the database portion, what is safe to skip in the readme?

[kwkroll32]

java disk quota exceeded, despite disk space available and quota not yet reached.
^ seems like upping the java memory may help? using a 100MB bam circumvents the problem

[kwkroll32]

index fasta file with samtools

[kwkroll32]

the java problem. hardcoded path to 1.7 into RNA-SeQC, leaving 1.8 set to the environment.
pipeline is not properly resuming from completed steps in the RNA-SeQC steps; can this be reproduced?

[kwkroll32]

pandas

[kwkroll32]

make picard memory options user configurable