Jennifer Hillman-Jackson

Enhancement: Tool panel search: If a tool is included in a tool group, let the tool be found with a search by the group label

1

**Describe the bug** When hunting for a tool, you might just remember the tool group label. Right now, searching with that label may or may not find the tools sorted...

Cuffdiff 2.2.1.5 SQLite option results in job failures

9

This is the most current version on the tool shed and it always fails when the SQLite option is used. History of the problem as it presented at https://usegalaxy.org: https://github.com/galaxyproject/usegalaxy-playbook/issues/50...

Enhance "Convert Characters" to include option to ignore chars in quotes

5

Some common CSV formatted files have content in double quotes. This can include commas. Conversion to tabular format is then difficult. Primary request to add in a option on the...

Update SICER to include more genome builds (ideally all on the instance)

2

The list of builds is outdated. At a minimum add the latest builds from the same organisms already included: mm10, hg38, dm6, sacCer3, rn5, rn6. The "pombe" and "tair8" are...

Tools work with Illumina 1.3-1.7 sequence identifiers plus any that have had /1 and /2 added, but do not work with default Illumina 1.8+ sequence identifiers. MTS Repos: https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer/effda79f510c https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_deinterlacer/462abc5618ba...

Details here: https://github.com/galaxyproject/galaxy/issues/4001 The problem is not new and has been reported since the tool was updated (~18 months ago). Not only is VCF input a problem for some, but...

Reference: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bowtie2_index_builder If a Bowtie2 index already exists, and a Tophat2 index is needed, the only DM available is the one above. **Issue** If Bowtie2 indexes already exists, a duplicate...

**Problem** Multi-select of inputs results in a combined job, instead of distinct jobs, and ends in failure. **Error** (presumably due to multiple BAM datasets sent as input): > bamtools filter...

Bamtools "Split" produces error

2

repo: tools-devteam/suites/suite_bamtools_2_3_0 https://toolshed.g2.bx.psu.edu/view/devteam/bamtools_split/71dd32fb0b0a produces an error on every dataset tested 7/21/2015 at usegalaxy.org. (not tested on latest cloudman in dev). original dataset sorted. re-sorting does not avoid the problem. one...

**Tool version** https://toolshed.g2.bx.psu.edu/view/devteam/picard/00fe2ff64467 **The default line length should be 80 (instead of 100)**. Some tools are picky about line length and 40-80 works with most. 100 is not accepted by...