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dib-lab / eel-pond

mRNAseq assembly, evaluation, and expression analysis
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PR status #38

Open johnsolk opened 7 years ago

johnsolk commented 7 years ago

Master branch has protocol steps 1-3 working. We need help reviewing and merging in steps 4-7. PR to review/merge:

Step 4: #25 (branch 'evaluation') Step 5: #27 (branch 'annotating') Step 6: #34 (branch 'salmon') Step 7: #37 (branch 'DE')

ctb commented 7 years ago

On Tue, Jan 17, 2017 at 01:42:26PM -0800, Lisa Cohen wrote:

Master branch has protocol steps 1-3 working. We need help reviewing and merging in steps 4-7. PR to review/merge:

Step 4: #25 (branch 'evaluation') Step 5: #27 (branch 'annoating') Step 6: #34 (branch 'salmon') Step 7: #37 (branch 'DE')

Hi @ljcohen, have you managed to run all four sets of instructions on one installed computer, or are there installation conflicts, do you know?

johnsolk commented 7 years ago

No conflicts as far as I'm aware. Yes, have run all on one installed computer. Step 5 uses a python 3 conda env, so there is a switch between envs. I'm unsure whether this is a good idea.

# after trinity
deactivate

source activate dammit
ctb commented 7 years ago

On Tue, Jan 17, 2017 at 01:55:37PM -0800, Lisa Cohen wrote:

No conflicts as far as I'm aware. Yes, have run all on one installed computer. Step 5 uses a python 3 conda env, so there is a switch between envs. I'm unsure whether this is a good idea.

OK - we can get it working all in one, and then try to simplify the install instructions afterwards. thx!