Daniel Blankenberg

Add when_empty attribute to tool outputs that can 'hide' or 'delete' …

4

…the item if it is empty at job completion.

[WIP] Enhance cut tool

6

... to allow use of step size within ranges, specifying the fill char, and allow handling headers in 3 different ways.

[WIP] Update cellxgene to enable setting options and saving created user annotations.

1

Todo - Should ensure a good way to terminate the running cellxgene server from inside - Requires an updated docker container to be made available

For example, this should include the original source URI for FASTA files and versions of software used to build indexes. Manual inspection of build logs, you can find versions for...

Issue found by @nvk747 This issue popped up when testing several tools at a time -- when the tests were run individually on the tools, they passed. I did not...

Consistency with Rpy 1 and NumPy packages and tools, e.g. linear_regression

4

These tools and dependency chains are broken. But will work if you have numpy 1.7 available locally. Detailed analysis follows. Rpy requires NumPy, but the current version of rpy 1.0.3...

GitHub and ToolShed are out of sync

2

There are changes in this repo that have not been pushed to the toolshed. This will cause **wasted effort** on bug tracking and fixing when fixes have already been merged...

Kraken Data Table Definition is improper

1

See: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/tool_data_table_conf.xml.sample and usage in https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/kraken.xml ``` bacteria_greengenes_rdp Bacteria_GreenGenes_RDP /path/to/data/kraken_database/bacteria_greengenes_rdp ``` Here, we have 3 columns defined `value, name, path`, where `value` is only ever used internally in Galaxy (good...

Dependency package needed for TwoBit Data Manager

9

Currently listed as requiring 'ucsc_tools', needs to have TS installable package that provides the 'faToTwoBit' executable.