Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Addition of IGV display for genome fasta file #3327

Merged
merged 4 commits into from Dec 16, 2016

Conversation

Projects
None yet
2 participants
@Delphine-L
Copy link
Contributor

commented Dec 16, 2016

Addition of IGV view for fasta files, allowing to load it as a genome in IGV display. In order to do that, implementation of the fai datatype and the fasta to fai converter

@@ -62,12 +62,16 @@
<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
<datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="True" display_in_upload="False"/>
<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
<datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="True" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html">
</datatype>

This comment has been minimized.

Copy link
@blankenberg

blankenberg Dec 16, 2016

Member

Probably a bit cleaner to do this as one line as <datatype .... />

@blankenberg blankenberg added this to the 17.01 milestone Dec 16, 2016

@blankenberg blankenberg merged commit a504e8e into galaxyproject:dev Dec 16, 2016

4 checks passed

api test Build finished. 244 tests run, 0 skipped, 0 failed.
Details
continuous-integration/travis-ci/pr The Travis CI build passed
Details
framework test Build finished. 132 tests run, 0 skipped, 0 failed.
Details
toolshed test Build finished. 580 tests run, 0 skipped, 0 failed.
Details
@blankenberg

This comment has been minimized.

Copy link
Member

commented Dec 16, 2016

Thanks for the contribution!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.