Commit dae026f5 authored by David M. Rogers's avatar David M. Rogers
Browse files

more doc. updates

parent e5e951f1
......@@ -60,4 +60,6 @@
* ran redis fill/empty test for listing ds
* v 0.1
* test the run_ad.sh script on 1 docking shard
* Test the run_ad.sh script on 1 docking shard.
This is a modified version of a fireworks script from
Swen Boehm (ORNL).
......@@ -56,11 +56,16 @@ to make this simpler in the future.
### Python/Anaconda Environment Setup
* Python Packages
* redis
* pandas
* numpy
* oddt
* Python Packages
* redis
* pandas
* numpy
* oddt
ODDT is only required by the `rescore` scripts. I ended up
installing this with Anaconda and using a separate environment
for it. That environment still needs all the other packages
above.
# Files Included
......@@ -106,11 +111,7 @@ DB Interaction Helpers:
* `setdb.py` -- load new jobs into the task db
Python imports for all codes:
* numpy -- I installed these using pip in a python3 venv
* pandas
* redis -- this is the python client API (https://pypi.org/project/redis/)
Rescore imports:
* oddt -- I installed this with Anaconda
* don't forget the above libraries too!
* numpy -- I installed these using pip in a python3 venv
* pandas
* redis -- this is the python client API (https://pypi.org/project/redis/)
1. change file naming scheme to something more user-defined
#. Fix shutdown process in rescore.py so that errors don't cause it to hang!
2. curate complete dataset for each job type [1h]
#. change file naming scheme to something more user-defined
#. curate complete dataset for each job type [1h]
- fix input tarballs on Summit
3. build & run test jobs for each jobtype [3h]
#. build & run test jobs for each jobtype [3h]
- small database (e.g. enamine diversity)
- protein point & click
4. Create python worker that attaches to job-db API [2h]
#. Change rescoring calculation to use GPU-accelerated contact
code @ https://github.com/scottlegrand/contacts
#. Create python worker that attaches to job-db API [2h]
using ZeroMQ
- make this transport agnostic and test on Summit
6. add FAQ on common error conditions
#. add FAQ on common error conditions
- protein conversion error
- docking step failure (reset & rerun scripts)
7. consolidate docking codebase
#. consolidate docking codebase
8. create separate directory per work item,
#. create separate directory per work item,
so stage-in/out can be completed asynchronously
*. create status query scripts parameterized over
#. create status query scripts parameterized over
jobtype (i.e. database name)
- tabled, since query script accepts db ID
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