Releases · hoffmangroup/genomedata

This release addresses long standing issues with builds and legacy Python support. Genomedata will now only support a minimum Python version of 3.7. Future releases will be easier to install and support. With the release of wheel builds, development tools and libraries are no longer necessary for Genomedata to be installed. It is still recommended that users install with Bioconda.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

required Python is now >=3.7
genomedata-load-data: changed to a python script with a c-extension

Known Bugs
To see all known bugs head to the issue tracker

This release addresses loading in sequence data where chromosome names do not have a UCSC-style name. In these cases, we have added the ability to give a tab-delimited file with a commented header (denoted with '#') to map between naming styles. This is the format used by NCBI and their assembly reports. Here is an example of an assembly report for hg38 from NCBI. You may choose what chromosome naming style you wish based on the given tab-delimited files. By default, chromosome names will attempt to map to UCSC-style names when given a tab-delimited file.

Here is a full list of changes made since the last announcement here:

Enhancements:

genomedata-load-seq: add chromosome name mapping based on assembly reports

Bug Fixes:

genomedata-load-data: fix bad error message when loading process fails

Known Bugs
To see all known bugs head to the issue tracker

Releases: hoffmangroup/genomedata

Genomedata 1.6.0

Genomedata 1.5.0