I installed all the tools on a clean galaxy instance based on all the workflows (workflow-to-tools + shed-tools install) + installed all the workflows itself and went trough all them manually, revealing following issues:
contributing
create-new-tutorial
Find Exons with the highest number of SNPs (or other features)
example-workflow.ga
Step 4: Group\
No value found for 'Operation 1 > Replace non numeric data'.\
Step 5: Group\
No value found for 'Operation 1 > Replace non numeric data'.
epigenetics
estrogen-receptor-binding-site-identification
Identification of the binding sites of the Estrogen receptor - chip-seq
chip_seq.ga
Step 13: plotFingerprint\
At least 1 datasets are required. Using default: ''.\
Step 21: multiBamSummary\
At least 2 datasets are required. Using default: ''.\
Step 22: computeMatrix\
At least 1 datasets are required. Using default: ''.\
Step 23: computeMatrix\
At least 1 datasets are required. Using default: ''.
epigenetics
methylation-seq
workflow-methylation-seq
methylation-seq.ga
Step 19: computeMatrix\
At least 1 datasets are required. Using default: ''.\
Step 21: computeMatrix\
At least 1 datasets are required. Using default: ''.
proteomics
database-handling
Database Handling Tutorial Workflow2 including Mycoplasma
wf_database-handling_mycoplasma.ga
Step 3: Protein Database Downloader\
An invalid option was selected for taxon, u'2148', please verify. Using default: '9606'.\
Step 4: Protein Database Downloader\
An invalid option was selected for taxon, u'2094', please verify. Using default: '9606'.\
Step 5: Protein Database Downloader\
An invalid option was selected for taxon, u'2115', please verify. Using default: '9606'.\
Step 6: Protein Database Downloader\
An invalid option was selected for taxon, u'2098', please verify. Using default: '9606'.\
Step 7: Protein Database Downloader\
An invalid option was selected for taxon, u'2100', please verify. Using default: '9606'.\
Step 8: Protein Database Downloader\
An invalid option was selected for taxon, u'2121', please verify. Using default: '9606'.
proteomics
protein-id-sg-ps
ProteinID_SG_PS_Tutorial_WF_datasetCollection
wf_proteinID_SG_PS_multipleFiles.ga
Step 6: Peptide Shaker\
No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.
proteomics
protein-id-sg-ps
Peptide and Protein ID Tutorial
wf_proteinID_SG_PS.ga
Step 6: Peptide Shaker\
No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.
proteomics
protein-id-oms
Peptide and Protein ID via OMS using two search engines
workflow_two-search-engines.ga
Step 7: IDMerger\
No value found for 'Input files separated by blanks'. Using default: ''.
statistics
age-prediction-with-ml
age_prediction_rna_seq (imported from uploaded file)
age-prediction-rna.ga
Step 4: Parallel Coordinates Plot\
No value found for 'All the dimensions in categorized datatype:'. Using default: 'True'.
transcriptomics
scrna-scanpy-pbmc3k
Clustering 3K PBMCs with Scanpy
main_workflow.ga
Step 5: Import Anndata and loom\
No value found for 'obs_names'. Using default: 'CellID'.\
No value found for 'Annotated data matrix'. Using default: ''.\
No value found for 'Is the data matrix to read sparse?'. Using default: 'True'.\
No value found for 'var_names'. Using default: 'Gene'.\
No value found for 'Cleanup?'. Using default: 'False'.\
No value found for 'X_name'. Using default: 'spliced'.\
No value found for 'hd5 format to be created'. Using default: 'anndata'.\
No value found for 'Format for the annotated data matrix'. Using default: 'loom'.
transcriptomics
de-novo
transcriptomics-denovo-workflow
transcriptomics-denovo-workflow.ga
Step 44: DESeq2\
No value found for '(Optional) provide a tabular file with additional batch factors to include in the model.'. Using default: ''.
visualisation
circos
asdf
main_workflow.ga
Step 3: Circos\
No value found for 'Reverse these Chromosomes'.\
No value found for 'Skip first label'. Using default: 'False'.\
No value found for 'Convert bands from BED format to circos karyotype band format'. Using default: 'True'.\
No value found for 'Skip last label'. Using default: 'False'.\
No value found for 'Cytogenetic Bands'. Using default: ''.\
No value found for 'Limit/Filter Chromosomes'.\
No value found for 'Ideogram Color Scheme'. Using default: 'paired-12-qual'.
I don't know which need to be solved, and how we could to this the fastest?
gallardoalba
commented
3 years ago
I installed all the tools on a clean galaxy instance based on all the workflows (
workflow-to-tools+shed-tools install) + installed all the workflows itself and went trough all them manually, revealing following issues:Step 4: Group\ No value found for 'Operation 1 > Replace non numeric data'.\ Step 5: Group\ No value found for 'Operation 1 > Replace non numeric data'.
Step 13: plotFingerprint\ At least 1 datasets are required. Using default: ''.\ Step 21: multiBamSummary\ At least 2 datasets are required. Using default: ''.\ Step 22: computeMatrix\ At least 1 datasets are required. Using default: ''.\ Step 23: computeMatrix\ At least 1 datasets are required. Using default: ''.
Step 19: computeMatrix\ At least 1 datasets are required. Using default: ''.\ Step 21: computeMatrix\ At least 1 datasets are required. Using default: ''.
Step 3: Protein Database Downloader\ An invalid option was selected for taxon, u'2148', please verify. Using default: '9606'.\ Step 4: Protein Database Downloader\ An invalid option was selected for taxon, u'2094', please verify. Using default: '9606'.\ Step 5: Protein Database Downloader\ An invalid option was selected for taxon, u'2115', please verify. Using default: '9606'.\ Step 6: Protein Database Downloader\ An invalid option was selected for taxon, u'2098', please verify. Using default: '9606'.\ Step 7: Protein Database Downloader\ An invalid option was selected for taxon, u'2100', please verify. Using default: '9606'.\ Step 8: Protein Database Downloader\ An invalid option was selected for taxon, u'2121', please verify. Using default: '9606'.
Step 6: Peptide Shaker\ No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.
Step 6: Peptide Shaker\ No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.
Step 7: IDMerger\ No value found for 'Input files separated by blanks'. Using default: ''.
Step 4: Parallel Coordinates Plot\ No value found for 'All the dimensions in categorized datatype:'. Using default: 'True'.
Step 5: Import Anndata and loom\ No value found for 'obs_names'. Using default: 'CellID'.\ No value found for 'Annotated data matrix'. Using default: ''.\ No value found for 'Is the data matrix to read sparse?'. Using default: 'True'.\ No value found for 'var_names'. Using default: 'Gene'.\ No value found for 'Cleanup?'. Using default: 'False'.\ No value found for 'X_name'. Using default: 'spliced'.\ No value found for 'hd5 format to be created'. Using default: 'anndata'.\ No value found for 'Format for the annotated data matrix'. Using default: 'loom'.
Step 44: DESeq2\ No value found for '(Optional) provide a tabular file with additional batch factors to include in the model.'. Using default: ''.
Step 3: Circos\ No value found for 'Reverse these Chromosomes'.\ No value found for 'Skip first label'. Using default: 'False'.\ No value found for 'Convert bands from BED format to circos karyotype band format'. Using default: 'True'.\ No value found for 'Skip last label'. Using default: 'False'.\ No value found for 'Cytogenetic Bands'. Using default: ''.\ No value found for 'Limit/Filter Chromosomes'.\ No value found for 'Ideogram Color Scheme'. Using default: 'paired-12-qual'.
I don't know which need to be solved, and how we could to this the fastest?