GTN Proteogenomics1 Database Creation
proteomics-proteogenomics-dbcreation/galaxy-workflow-mouse-rnaseq-dbcreation
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flowchart TD 0["ℹ️ Input Dataset\nFASTQ_ProB_22LIST.fastqsanger"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nMus_musculus.GRCm38.86.gtf"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nTrimmed_ref_5000_uniprot_cRAP.fasta"]; style 2 stroke:#2c3143,stroke-width:4px; 3["HISAT2"]; 0 -->|output| 3; 4["Editing GTF File"]; 1 -->|output| 4; 70b6f719-803f-4fa9-8394-a3b64b71ec01["Output\nchr_corrected_gtf"]; 4 --> 70b6f719-803f-4fa9-8394-a3b64b71ec01; style 70b6f719-803f-4fa9-8394-a3b64b71ec01 stroke:#2c3143,stroke-width:4px; 5["FASTA-to-Tabular"]; 2 -->|output| 5; 6["FreeBayes"]; 3 -->|output_alignments| 6; 7["StringTie"]; 4 -->|outfile| 7; 3 -->|output_alignments| 7; 8["Filter Tabular"]; 5 -->|output| 8; 9["CustomProDB"]; 3 -->|output_alignments| 9; 6 -->|output_vcf| 9; 10["GffCompare"]; 4 -->|outfile| 10; 7 -->|output_gtf| 10; 11["SQLite to tabular"]; 9 -->|output_genomic_mapping_sqlite| 11; 12["SQLite to tabular"]; 9 -->|output_variant_annotation_sqlite| 12; 13["FASTA Merge Files and Filter Unique Sequences"]; 9 -->|output_rpkm| 13; 9 -->|output_snv| 13; 9 -->|output_indel| 13; a5054be9-dd74-4d60-a4c6-494fdbcb97a1["Output\nCustomProDB_FASTA"]; 13 --> a5054be9-dd74-4d60-a4c6-494fdbcb97a1; style a5054be9-dd74-4d60-a4c6-494fdbcb97a1 stroke:#2c3143,stroke-width:4px; 14["FASTA-to-Tabular"]; 9 -->|output_rpkm| 14; 15["Convert gffCompare annotated GTF to BED"]; 10 -->|transcripts_annotated| 15; 16["Column Regex Find And Replace"]; 11 -->|query_results| 16; 17["Column Regex Find And Replace"]; 12 -->|query_results| 17; 18["FASTA-to-Tabular"]; 13 -->|output| 18; 19["Filter Tabular"]; 14 -->|output| 19; 20["Translate BED transcripts"]; 15 -->|output| 20; 21["Query Tabular"]; 17 -->|out_file1| 21; e9468479-4ebd-4ced-8086-c10e916b97c5["Output\nvariant_annoation_sqlite"]; 21 --> e9468479-4ebd-4ced-8086-c10e916b97c5; style e9468479-4ebd-4ced-8086-c10e916b97c5 stroke:#2c3143,stroke-width:4px; 22["Column Regex Find And Replace"]; 18 -->|output| 22; 23["Reference Protein Accessions"]; 19 -->|output| 23; 8 -->|output| 23; 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85["Output\nReference_Protein_Accessions"]; 23 --> 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85; style 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85 stroke:#2c3143,stroke-width:4px; 24["bed to protein map"]; 20 -->|translation_bed| 24; 25["Tabular-to-FASTA"]; 22 -->|out_file1| 25; 26["Concatenate datasets"]; 24 -->|output| 26; 16 -->|out_file1| 26; 27["FASTA Merge Files and Filter Unique Sequences"]; 2 -->|output| 27; 25 -->|output| 27; 20 -->|translation_fasta| 27; 924bce7c-5c6a-4cb3-a459-18784a55ae01["Output\nUniprot_cRAP_SAV_indel_translatedbed_FASTA"]; 27 --> 924bce7c-5c6a-4cb3-a459-18784a55ae01; style 924bce7c-5c6a-4cb3-a459-18784a55ae01 stroke:#2c3143,stroke-width:4px; 28["Genomic_mapping_sqlite"]; 26 -->|out_file1| 28; 6542c4e5-289a-4be4-9b42-7a4e170ba198["Output\ngenomic_mapping_sqlite"]; 28 --> 6542c4e5-289a-4be4-9b42-7a4e170ba198; style 6542c4e5-289a-4be4-9b42-7a4e170ba198 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | FASTQ_ProB_22LIST.fastqsanger |
Input dataset | Mus_musculus.GRCm38.86.gtf |
Input dataset | Trimmed_ref_5000_uniprot_cRAP.fasta |
Outputs
From | Output | Label |
---|---|---|
Input dataset | FASTQ_ProB_22LIST.fastqsanger | |
Input dataset | Mus_musculus.GRCm38.86.gtf | |
Input dataset | Trimmed_ref_5000_uniprot_cRAP.fasta | |
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5 | HISAT2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | Editing GTF File |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | FASTA-to-Tabular | |
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1 | FreeBayes | |
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1 | StringTie | |
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 | Filter Tabular | |
toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0 | CustomProDB | |
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2 | GffCompare | |
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 | SQLite to tabular | |
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 | SQLite to tabular | |
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 | FASTA Merge Files and Filter Unique Sequences | |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | FASTA-to-Tabular | |
toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1 | Convert gffCompare annotated GTF to BED | |
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0 | Column Regex Find And Replace | |
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0 | Column Regex Find And Replace | |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | FASTA-to-Tabular | |
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 | Filter Tabular | |
toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0 | Translate BED transcripts | |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 | Query Tabular | |
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0 | Column Regex Find And Replace | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 | Concatenate datasets | Reference Protein Accessions |
toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0 | bed to protein map | |
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 | Tabular-to-FASTA | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 | Concatenate datasets | |
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 | FASTA Merge Files and Filter Unique Sequences | |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 | Query Tabular | Genomic_mapping_sqlite |
Tools
To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.
Importing into Galaxy
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!Hands-on: Importing a workflow
- Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
- Click on galaxy-upload Import at the top-right of the screen
- Provide your workflow
- Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
- Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
- Click the Import workflow button
Below is a short video demonstrating how to import a workflow from GitHub using this procedure:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
12 | 28fc28c45 | 2021-02-08 19:18:49 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
11 | 1eca54ca9 | 2021-01-27 21:47:56 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
10 | 0db38ae94 | 2021-01-27 21:41:38 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
9 | 13e2ffc4d | 2021-01-27 21:27:34 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
8 | 2c4b4646c | 2021-01-27 21:17:15 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
7 | f99b54e3c | 2021-01-27 21:01:48 | Update galaxy-workflow-mouse_rnaseq_dbcreation.ga |
6 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
5 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
4 | 55fe079b2 | 2020-01-13 16:30:56 | WoLF PSORT WF |
3 | 361236c41 | 2019-04-04 09:00:14 | Changed format of workflows |
2 | 6eef55b7e | 2019-02-27 18:54:36 | Updated install_tutorial_requirements.sh + minor fixes (#1275) |
1 | a928824de | 2018-08-25 09:12:50 | add protegenomics dbcreation tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga -O workflow.ga workflow-to-tools -w workflow.ga -o tools.yaml shed-tools install -g GALAXY -a API_KEY -t tools.yaml workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows