Releases: knights-lab/shi7
SHI7: SHort-read Iterative Trimmer with Learning Module
SHI7: SHort-read Iterative Trimmer with Learning Module
What is new:
- Fixed the conda recipe
SHI7: SHort-read Iterative Trimmer with Learning Module
Portable edition of v1.0.0 ("portable" branch direct mirror).
This version resolves the installation and build problems with the conda release. Instructions for installation are simple:
- Ensure you have java and python installed
- Extract the contents of the release package
- Add the extracted directory to your PATH
So, for example, from your home directory or another directory you want to install shi7 into:
unzip shi7_portable_linux_v1.0.1.zip
PATH=$PWD/shi7:$PATH
That's it. These instructions unzipped the package, creating a folder called "shi7" in your current directory, and added that new "shi7" folder to your active system path. You should now be able to run "shi7.py" and "shi7_learning.py" from the commandline.
Before you exit or change directories, if you want to add shi7 "permanently" to your bash terminal (so there will be no need to run the above steps again the next time you want to use shi7):
echo "PATH=$PWD/shi7:$PATH" >> ~/.bashrc
This creates a line in your terminal configuration that will tell it where shi7 is always located.
To update to newer versions of shi7, simply extract and drop the contents of any new release's zip file into the same folder as you created above, no need to run anything extra.
SHI7: SHort-read Iterative Trimmer with Learning Module
What is new:
- Update to allow Python 3.7+
- Now throws a warning if the trim length is less than 50 and throws an error if it is less than 5
SHI7: SHort-read Iterative Trimmer with Learning Module
What's new:
- Now outputs a text file that lists all learned options
SHI7: SHort-read Iterative Trimmer with Learning Module
What's new
Updated the Makefile
Please cite this article if you use SHI7:
SHI7: SHort-read Iterative Trimmer with Learning Module
What's new
Minor bugfixes and changes to paired end mode -- now when output is not combined (and SE is not specified) the trimming will keep the resulting pairs in sync.
Please cite this article if you use SHI7:
SHI7: SHort-read Iterative Trimmer with Learning Module
Putting releases in sync with conda.
Portable editions unchanged (still on 0.9.3 branch but functionally near-identical)
SHI7: SHort-read Iterative Trimmer with Learning Module
What
Minor bugfixes in portable release (v0.93 branch). Conda release coming soon!
- SE flag wasn't being detected properly in some cases
- Fixed some bugs with relative paths
Please cite this article if you use SHI7:
SHI7: SHort-read Iterative Trimmer (and Learning Module) v0.9.3b
What
Bugfixes to the v0.9.3 branch:
- os.link replaced with os.symlink (supports cross-disk talk)
- fixed incorrect detection of SE flag in shi7.py under certain conditions
- adjusted the stitching range parameter learning
- fixed a bug in handling odd numbers of SE reads