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…-1736903391 Add missing data-library.yaml files
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topics/proteomics/tutorials/neoantigen-1-fusion-database-generation/data-library.yaml
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|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 1: Fusion-Database-Generation' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14365542' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14365542/files/human_reference_genome.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14365542 | ||
| - url: https://zenodo.org/record/14365542/files/RNA-Seq_Reads_1.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14365542 | ||
| - url: https://zenodo.org/record/14365542/files/human_reference_genome_annotation.gtf | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14365542 | ||
| - url: https://zenodo.org/record/14365542/files/RNA-Seq_Reads_2.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14365542 | ||
| - url: https://zenodo.org/record/14365542/files/Arriba-Fusion-Database.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14365542 |
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topics/proteomics/tutorials/neoantigen-2-non-normal-database-generation/data-library.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 2: Non-normal-Database-Generation' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14372521' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14372521/files/Homo_sapiens.GRCh38_canon.106.gtf | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14372521 | ||
| - url: https://zenodo.org/record/14372521/files/HUMAN_CRAP.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14372521 | ||
| - url: https://zenodo.org/record/14372521/files/RNA-Seq_Reads_1.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14372521 | ||
| - url: https://zenodo.org/record/14372521/files/GffCompare_Annotated_GTF_to_BED.bed | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14372521 | ||
| - url: https://zenodo.org/record/14372521/files/RNA-Seq_Reads_2.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14372521 | ||
| - url: https://zenodo.org/record/14372521/files/Human_cRAP_Non_normal_transcripts_dB_generation.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14372521 |
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topics/proteomics/tutorials/neoantigen-3-fragpipe-discovery/data-library.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 3: Database merge and FragPipe discovery' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14374118' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14374118/files/Arriba-Fusion-Database.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 | ||
| - url: https://zenodo.org/record/14374118/files/STS_26T_2_Eclipse_02102024.raw | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 | ||
| - url: https://zenodo.org/record/14374118/files/Human_cRAP_Non_normal_transcripts_dB.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 | ||
| - url: https://zenodo.org/record/14374118/files/Experimental-Design-Fragpipe.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 | ||
| - url: https://zenodo.org/record/14374118/files/Fragpipe-Peptide-Report.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 | ||
| - url: https://zenodo.org/record/14374118/files/Neoantigen_Peptide_Candidates_for_PepQuery.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14374118 |
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topics/proteomics/tutorials/neoantigen-4-peptide-verification/data-library.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 4: PepQuery2 Verification' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14375467' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14375467/files/STS_26T_2_Eclipse_02102024.raw | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375467 | ||
| - url: https://zenodo.org/record/14375467/files/Human-TaxID.txt | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375467 | ||
| - url: https://zenodo.org/record/14375467/files/NeoAntigen-Candidates.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375467 | ||
| - url: https://zenodo.org/record/14375467/files/Novel_Peptides_from_PepQuery.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375467 | ||
| - url: https://zenodo.org/record/14375467/files/HUMAN_CRAP.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375467 |
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topics/proteomics/tutorials/neoantigen-5-variant-annotation/data-library.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 5: Variant Annotation' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14375693' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14375693/files/Fragpipe-Peptide-Report.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375693 | ||
| - url: https://zenodo.org/record/14375693/files/GffCompare_Annotated_GTF_to_BED.bed | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375693 | ||
| - url: https://zenodo.org/record/14375693/files/Novel_Peptides_from_PepQuery.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375693 | ||
| - url: https://zenodo.org/record/14375693/files/Neoantigen_summary.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375693 | ||
| - url: https://zenodo.org/record/14375693/files/Homo_sapiens.GRCh38_canon.106.gtf | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375693 |
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topics/proteomics/tutorials/neoantigen-6-predicting-hla-binding/data-library.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 6: Predicting HLA Binding' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14375917' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14375917/files/RNA-Seq_Reads_2.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14375917 | ||
| - url: https://zenodo.org/record/14375917/files/RNA-Seq_Reads_1.fastqsanger.gz | ||
| src: url | ||
| ext: fastqsanger.gz | ||
| info: https://doi.org/10.5281/zenodo.14375917 | ||
| - url: https://zenodo.org/record/14375917/files/IEDB_seq2HLA_alleles.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375917 | ||
| - url: https://zenodo.org/record/14375917/files/IEDB-Optitype-seq2HLA-alleles.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375917 | ||
| - url: https://zenodo.org/record/14375917/files/IEDB_Optitype_alleles.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14375917 |
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topics/proteomics/tutorials/neoantigen-7-hla-binding-novel-peptides/data-library.yaml
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| --- | ||
| destination: | ||
| type: library | ||
| name: GTN - Material | ||
| description: Galaxy Training Network Material | ||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||
| items: | ||
| - name: Proteomics | ||
| description: Training material for proteomics workflows in Galaxy | ||
| items: | ||
| - name: 'Neoantigen 7: IEDB binding PepQuery Validated Neopeptides' | ||
| items: | ||
| - name: 'DOI: 10.5281/zenodo.14377365' | ||
| description: latest | ||
| items: | ||
| - url: https://zenodo.org/record/14377365/files/STS_26T_2_Eclipse_02102024.mgf | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/iedb_novel_peptide_x_hla_table-weak.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/iedb_predicted_neoantigens-strong.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/FASTA-IEDB.fasta | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/iedb_novel_peptide_x_hla_table-strong.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/iedb_predicted_neoantigens-weak.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 | ||
| - url: https://zenodo.org/record/14377365/files/IEDB-Optitype-seq2HLA-alleles.tabular | ||
| src: url | ||
| ext: | ||
| info: https://doi.org/10.5281/zenodo.14377365 |