Is there a list of new features requested or bugs that need to be fixed. How would developers contribute if the were just getting involved on some volenteer part time basis?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Hello Ashreid,
We would love to have more people contributing to the codebase.
Getting started, I would first make sure you can:- Clone the source from github and build openge (See the developer docs for compilation instructions)
- Run the tests (make test)
- Branch the source so you have something to develop against
We don't have a public list of features and bugs to work on, but here are a couple of things off the top of my head:- Add additional testing. Most of the built in tests simply execute openge with valid inputs, but don't check the output of tests. More robust testing would be useful to us. Check out run.sh from this test that I just checked in for an example: here
I have been meaning to verify that we have full test coverage for both SAM and BAM inputs, being passed in as a filename, as well as piped into OpenGE. A good test (or set of tests) would verify that we can run:
Code:cat asdf.bam | ./openge count
Code:./openge asdf.bam
Code:./openge count < asdf.bam.
- The CMake build system supports building packages for linux platforms (see here). It would be great if we could build .deb and .rpm packages with a command that included the appropriate binary and referenced necessary dependencies.
- Additional features. If you're interested on working on additional features, we will need to coordinate with David (adaptivegenome). He's the guy in charge of deciding what goes into openge.
If you have patches to contribute, please branch the openge source on github and submit a pull request with your modifications and we'll have a look.
-Lee
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment