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genomes_UCSC.data.yaml
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genomes_UCSC.data.yaml
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genomes:
- genome_id: human_dec2013_hg38_ucsc
name: Human Dec. 2013 (GRCh38/hg38)
build_id: human_dec2013_hg38_ucsc_genome
ucsc_key: hg38
fasta_url: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz
- dbkey: dm6_UCSC_2014_10_14_BDGP_6_plus_ISO1_MT
name: Drosophila melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
build_id: dm6
fasta_url: http://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
# not sure about this mrna file, dont really
#cdna_dbkey: dm6_UCSC_2014_10_14_BDGP_6_plus_ISO1_MT_mrna
#cdna_build_id: dm6_UCSC_2014_10_14_BDGP_6_plus_ISO1_MT_mrna
#cdna_fasta_url: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/mrna.fa.gz
#annotation_id: dm6_UCSC_2014_10_14_BDGP_6_plus_ISO1_MT_gff3
#annotation_url:
# dont have a public url for the annotation?
- genome_id: mouse_dec2011_mm10_ucsc
name: Mouse Dec. 2011 (GRCm38/mm10)
build_id: mouse_dec2011_mm10_ucsc_genome
ucsc_key: mm10
fasta_url: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz
- genome_id: mouse_jun2020_mm39_ucsc
name: Mouse Jun. 2020 (GRCm39/mm39)
build_id: mouse_jun2020_mm39_ucsc_genome
ucsc_key: mm39
fasta_url: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chromFa.tar.gz
data_managers:
#Load the genome fasta
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4
params:
- 'dbkey_source|dbkey_source_selector': 'new'
- 'dbkey_source|dbkey': '{{ item.dbkey }}'
- 'dbkey_source|dbkey_name': '{{ item.name }}'
- 'reference_source|reference_source_selector': 'url'
- 'reference_source|user_url': '{{ item.fasta_url }}'
- 'sequence_name': '{{ item.name }} - Genome'
- 'sequence_id': '{{ item.build_id }}'
- 'sorting|sorting_selector': 'as_is'
items: "{{ genomes }}"
data_table_reload:
- all_fasta
- __dbkeys__
# #Build bowtie2 index using the genome fasta
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.3.5.1+galaxy1
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }} - Genome'
- 'sequence_id': '{{ item.build_id }}'
items: "{{ genomes }}"
data_table_reload:
- bowtie2_indexes
#- tophat2_indexes
- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/2.7.4a
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'name': '{{ item.name }} - splice junctions NOT included'
- 'GTFconditional|GTFselect': 'withoutGTF'
items: "{{ genomes }}"
data_table_reload:
- rnastar_index2x_versioned
# this creates indexes for the older versions of star
- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/0.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'name': '{{ item.name }} - splice junctions NOT included'
- 'GTFconditional|GTFselect': 'withoutGTF'
items: "{{ genomes }}"
data_table_reload:
- rnastar_index2
#Build HISAT2 INDEX
- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/2.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }}'
- 'sequence_id': '{{ item.build_id }}'
items: "{{ genomes }}"
data_table_reload:
- hisat2_indexes
# Build bwa index using the genome fasta
#- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.3
#- id: bwa_mem_index_builder_data_manager
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }}'
- 'sequence_id': '{{ item.build_id }}'
- 'index_algorithm': 'bwtsw'
items: "{{ genomes }}"
data_table_reload:
- bwa_mem_indexes
#Load the genome fasta
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4
params:
- 'dbkey_source|dbkey_source_selector': 'new'
- 'dbkey_source|dbkey': '{{ item.genome_id }}'
- 'dbkey_source|dbkey_name': '{{ item.name }}'
- 'reference_source|reference_source_selector': 'url'
- 'reference_source|user_url': '{{ item.fasta_url }}'
- 'sequence_name': '{{ item.name }}'
- 'sequence_id': '{{ item.build_id }}'
- 'sorting|sorting_selector': 'as_is'
items: "{{ genomes }}"
data_table_reload:
- all_fasta
- __dbkeys__
# Build bowtie2 index using the genome fasta
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.3.5.1+galaxy1
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }}'
- 'sequence_id': '{{ item.build_id }}'
items: "{{ genomes }}"
data_table_reload:
# Bowtie creates indices for Bowtie and TopHat
- bowtie2_indexes
- tophat2_indexes
#Build STAR index (no GFF)
- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/0.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'name': '{{ item.name }} - splice junctions NOT included'
- 'GTFconditional|GTFselect': 'withoutGTF'
items: "{{ genomes }}"
data_table_reload:
- rnastar_index2
#Build HISAT2 INDEX
- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/2.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }} - splice junctions NOT included'
- 'sequence_id': '{{ item.build_id }}'
items: "{{ genomes }}"
data_table_reload:
- hisat2_indexes
## Build bwa index using the genome fasta
#- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.3
#- id: bwa_mem_index_builder_data_manager
- id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5
params:
- 'all_fasta_source': '{{ item.build_id }}'
- 'sequence_name': '{{ item.name }}'
- 'sequence_id': '{{ item.build_id }}'
- 'index_algorithm': 'bwtsw'
items: "{{ genomes }}"
data_table_reload:
- bwa_mem_indexes