galaxyproject/tools-devteam

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Contains a set of Galaxy Tools mostly written by the Galaxy Team.

Stars: 37
Forks: 94
Open beginner issues: 0
Indexed issues: 60

Dominant language: Python
License: No license data
Last GitHub push: Jul 30, 2026
Latest indexed: Sep 16, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

60 open issues indexed

Add citations to all the tools. Open

enhancement

galaxyproject/tools-devteam#3 · 10 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Make Tools Collection-Aware Open

enhancement

galaxyproject/tools-devteam#26 · 17 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
picard_BamIndexStats.xml and rgPicardHsMetrics.xml missing Open

bug

galaxyproject/tools-devteam#45 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
cuffmerge/cufflinks wrapper state handling Open

bug

galaxyproject/tools-devteam#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Dependency package needed for TwoBit Data Manager Open

enhancement

galaxyproject/tools-devteam#94 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
vcftools dependencies: tabix and bgzip Open

bug

galaxyproject/tools-devteam#111 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
bowtie2 index data manager fails if index already exists Open

bug

galaxyproject/tools-devteam#127 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
fastq groomer does not parse sequence ids that contain spaces properly Open

bug

galaxyproject/tools-devteam#130 · 12 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Unsorted BAM input not parsed by sam_merge ("Merge BAM Files" in UI) Open

galaxyproject/tools-devteam#159 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
No change when using option "unsorted" as sort order with picard_sortsam Open

galaxyproject/tools-devteam#160 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
picard_SortSam and sam_sort appear to be performing the same operation Open

galaxyproject/tools-devteam#162 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
picard_MergeSAMFiles and sam_merge perform the same function Open

galaxyproject/tools-devteam#166 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Cuffquant (Galaxy Tool Version 2.2.1.0) tool vs tool form input mismatch Open

bug

galaxyproject/tools-devteam#170 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Sam_to_bam - make reference genome selection optional Open

galaxyproject/tools-devteam#174 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Bamtools "Split" produces error Open

bug

galaxyproject/tools-devteam#186 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Update Tophat for Collection-Aware Read Group Mapping Open

enhancement

galaxyproject/tools-devteam#202 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
samtools_mpileup fails when optional tag set is used Open

galaxyproject/tools-devteam#219 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Genome fetching data manager has incorrect "GATK" sort Open

galaxyproject/tools-devteam#241 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
populate all .shed.yaml with descriptions and synopses from MTS Open

galaxyproject/tools-devteam#246 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Enhance "Convert Characters" to include option to ignore chars in quotes Open

enhancement

galaxyproject/tools-devteam#250 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Remove sort_by from all reference select boxes Open

galaxyproject/tools-devteam#251 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Create a tool that will Group and Filter on multiple columns Open

galaxyproject/tools-devteam#260 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Readgroup assigment in bwa, bwa-mem, and bowtie2 and possible other tools does not set SM tag Open

bug

galaxyproject/tools-devteam#270 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
gffread is problematic in the main Tool Shed Open

bug

galaxyproject/tools-devteam#288 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Kraken Data Table Definition is improper Open

bug

galaxyproject/tools-devteam#292 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Custom reference genomes, bowtie fails to recognize Open

galaxyproject/tools-devteam#307 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Bwa-mem issues Open

bug

galaxyproject/tools-devteam#312 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Sam-merge error checking doesn't work well with BWA aligned reads Open

galaxyproject/tools-devteam#313 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Kraken installation via tool shed on Mac OSX 10.10.5 (for development) Open

bug

galaxyproject/tools-devteam#315 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modify Bowtie2 DM so that it will not create duplicates when "Include Tophat2" is used Open

enhancement

galaxyproject/tools-devteam#319 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Annovar produces green empty dataset when output set to VCF Open

bug

galaxyproject/tools-devteam#323 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Pileup datatype edit-attribute columns are a mismatch for type Open

galaxyproject/tools-devteam#329 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Generate pileup from BAM dataset - tool output tabular format, not pileup Open

galaxyproject/tools-devteam#330 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add CreateSequenceDictionary to Picard Tools Open

galaxyproject/tools-devteam#331 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
gops subtract broken Open

bug

galaxyproject/tools-devteam#333 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
BAMtools "Convert, Merge, Randomize" - "Random" option requires sorted input Open

galaxyproject/tools-devteam#338 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add option for "BAMTools Convert, Merge, Randomize" to process a collection as a group Open

galaxyproject/tools-devteam#339 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
cummeRbund 1.0.1 error - plots fail against sqlite database content Open

bug wip

galaxyproject/tools-devteam#340 · 9 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Clean up cuffdiff (maybe others) collection hacks. Open

galaxyproject/tools-devteam#342 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
How to access a genome fasta index (FAI) build with data_manager_sam_fasta_index_builder (qustion also on biostars) Open

galaxyproject/tools-devteam#362 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Rsync with G2 search function no longer functioning on latest build Open

galaxyproject/tools-devteam#387 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Update SICER to include more genome builds (ideally all on the instance) Open

enhancement software update

galaxyproject/tools-devteam#390 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
list of high profile tools to move to IUC Open

galaxyproject/tools-devteam#406 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Consistency with Rpy 1 and NumPy packages and tools, e.g. linear_regression Open

bug

galaxyproject/tools-devteam#415 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
GitHub and ToolShed are out of sync Open

galaxyproject/tools-devteam#416 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Picard FixMateInformation does not launch individual jobs when multiple datasets are selected Open

bug

galaxyproject/tools-devteam#421 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Enhance/normalize "Picard Normalize Fasta" default settings and better link-in custom genome formatting Open

enhancement

galaxyproject/tools-devteam#433 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Bamtools Filter BAM triggers a combined job instead of distinct jobs with version 2 Open

bug

galaxyproject/tools-devteam#440 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Adding MiniKrakenDB and SILVA to Kraken Data manager? Open

galaxyproject/tools-devteam#443 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Unsorted BAM output for bwa mem? Open

galaxyproject/tools-devteam#478 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026

galaxyproject/tools-devteam

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