This is a repository to contain computational challenges. Who can write the fastest fastq parser? Average phred qualities?
This is not necessarily limited to just speed and so challenges could include other computational metrics like memory.
Results can be found in RESULTS.md.
bash bin/run-challenges.shThis script will run all challenges.
Results of time (and any future benchmarks) will be in times/*.time/.
Sets of challenges will be defined as having the same categories.
bash bin/compare-challenges.sh
Challenge Contestant reps time(s)
countgc.time countGC-perl 10 .01
countgc.time countGC-python 10 .03
perl.time countGC-perl 10 .01
python.time countGC-python 10 .02In this example, someone could compare countGC-perl and countGC-python
to compare the countgc.time challenge.
Each challenge is in its own folder and needs to have standard naming. Some files are listed as reserved names so that you do not create it yourself.
Files you need to make
| file | description |
|---|---|
| run.sh | The shell script to run the test |
| input | The input file for the test. It can be in any format needed. It can be generated on the fly by run.sh. |
| categories.txt | A list of categories. Other tests with the same categories will be compared. Categories will be in all lowercase. |
| method | A folder containing all files pertaining to the actual method (optional) |
Files that have reserved names that you should not make.
| file | description |
|---|---|
| out | All output files and logs go to this directory, if they exist. If this directory does not exist, it will be created for you. |
| time.txt | This file will be created at the time of the test. |