Galaxy Community Help

Topic	Replies	Views	Activity
Anyone else having issues with Salmon Data Manager never installing? galaxy-local , salmon	9	23	September 23, 2024
snippy tutorial - snpeff step variant-analysis , snpeff_build_gb	9	8	June 11, 2025
What should I do if my data exceeds the given 250GB of storage? account , storage-dashboard , resources , manage-quota , scratch-space I’m working on a transciptomics data which will probably exceed the given 250GB data. Is there any possible solution to this? for example increasing my storage?	3	1467	August 15, 2024
Need help installing Galaxy: "ModuleNotFoundError: No module named 'lib2to3'" galaxy-local , troubleshooting	4	2138	January 16, 2025
AnnData Operations - AttributeError: 'DataFrame' object has no attribute 'dtype' single-cell	5	1294	August 7, 2024
Issues with UMI Tools deduplicate usegalaxy.org support tool-help , umi_tools_dedup	6	480	September 14, 2024
bedtools intersect intervals usegalaxy.eu support chip-seq , rna-seq	5	244	June 21, 2024
Adding Galaxy EU workflow to IWC Library - Planemo installation usegalaxy.eu support workflow , troubleshooting	7	50	November 19, 2024
BUSCO Fatal error: Exit code 1 () usegalaxy.eu support tool-help , busco	5	236	January 17, 2025
Kraken2 Databse for 16s full length metagenomics usegalaxy.eu support metagenomics	1	65	January 6, 2025
Kraken 2 core nt database and large amount of unclassified reads? usegalaxy.eu support reference-index , single-cell	6	349	January 8, 2025
nf-core Pipeline Integration to Local Galaxy workflow , tool-dev , planemo , nextflow	2	108	August 21, 2024
403 Errors and a site that "can't be reached" usegalaxy.org support upload , server-status	2	37	January 19, 2025
Decoupler on AnnData object from Scanpy - task fails usegalaxy.eu support tool-help , single-cell , decoupler_pseudobulk	3	313	July 12, 2024
Error when running DeSeq2: help resources and input strategies Resources transcriptomics , resources , tool-help , deseq2	3	294	August 30, 2024
PCA (Principal Component Analysis) plots from ChIP-seq data usegalaxy.org support chip-seq	3	283	June 20, 2024
How heavy is Galaxy right after installation? usegalaxy.eu support galaxy-local	4	49	September 17, 2024
DEseq2 understanding the log2 fold change usegalaxy.org support resources , tool-help , deseq2	3	290	September 27, 2024
Additional storage usegalaxy.org support scratch-space	3	282	July 1, 2024
DESeq2, using "age" as a continuous variable tool-help , deseq2	2	305	September 5, 2024
Need help trimming sample barcodes and sequencing adapters usegalaxy.org support single-cell	4	238	September 10, 2024
Slow uploads to usegalaxy.org usegalaxy.org support upload	1	117	February 7, 2025
MITOS2 understanding the output troubleshooting	5	207	July 1, 2024
convert fasta file to GFF/GTF	3	255	July 8, 2024
Release of Galaxy 24.2 news , release	2	15	February 14, 2025
ATAC-Seq Analysis Using MACS2 Callpeak usegalaxy.org support gtn-tutorial , atac-seq , picard_markduplicates	1	169	November 12, 2024
Maker and Braker 3 running for half a week - and still going usegalaxy.eu support troubleshooting , queued-gray-datasets	4	28	April 23, 2025
Problems using the scratch 1TB usegalaxy.org support account , scratch-space	6	156	October 7, 2024
How to add a new reference-genome on HISTAT2? I need S. agalactiae BM110 usegalaxy.eu support reference-genome	5	211	July 1, 2024
Help to evaluate my assembly results usegalaxy.eu support	1	49	July 17, 2024
What are the steps for preprocessing single cell data generated from BD Rhapsody system ? single-cell	2	40	May 2, 2025
cannot download files from history usegalaxy.org support download	1	25	January 19, 2025
Will Nanopore-related tools be updated to accept pod5 files? usegalaxy.eu support single-cell , variant-analysis	2	201	July 8, 2024
Troubleshooting Mageck Count genome-annotation	3	168	July 10, 2024
Conversion of a tar file to fastq format usegalaxy.org support upload	3	164	July 15, 2024
PICRUSt2 Full pipeline tool-help , picrust2_pipeline , picrust	4	146	November 7, 2024
FastQC Troubleshooting tool-help , quality-control , fastqc	4	141	August 26, 2024
Please run Megablast as an option with BLASTN usegalaxy.eu support mapping , blast , tool-help , ncbi_blastn_wrapper , megablast_wrapper	8	117	August 18, 2024
Whole Exome Sequencing workflow gtn-tutorial , workflow	4	149	August 30, 2024
libjemalloc.so.2: cannot allocate memory in static TLS block Error on Galaxy Startup server-admin , galaxy-local , exceeds-memory-error	1	217	November 13, 2024
User Account Quotas, Memory and Concurrent jobs at UseGalaxy.eu usegalaxy.eu support job-config , account , queued-gray-datasets , paused-jobs , resources	4	49	April 16, 2025
Resolved: Fatal error: Exit code 255 () with kraken2? usegalaxy.org support kraken2	5	127	September 24, 2024
Map With BWA-MEM not working with one particular reference genome usegalaxy.org support reference-index , server-open-issue	5	130	August 30, 2024
error with Picard's MarkDuplicates - This job was terminated because it used more memory than it was allocated. usegalaxy.org support picard , exceeds-memory-error	2	180	July 22, 2024
Error When Upgrading Database server-admin	4	29	March 24, 2025
data not uploading usegalaxy.eu support troubleshooting	7	106	November 25, 2024
Jobs running or queued for more than 48 hours usegalaxy.be support queued-gray-datasets	5	66	February 21, 2025
New error message: 'Failed - Forbidden' when trying to download data usegalaxy.org support troubleshooting	3	26	January 20, 2025
featureCounts- "An error occured with this data set" tool-help , featurecounts	2	174	June 20, 2024
How to turn .bam into VCF usegalaxy.org support freebayes	7	97	January 15, 2025

Anyone else having issues with Salmon Data Manager never installing?

galaxy-local , salmon

9

23

September 23, 2024

snippy tutorial - snpeff step

variant-analysis , snpeff_build_gb

9

8

June 11, 2025

What should I do if my data exceeds the given 250GB of storage?

account , storage-dashboard , resources , manage-quota , scratch-space

I’m working on a transciptomics data which will probably exceed the given 250GB data. Is there any possible solution to this? for example increasing my storage?