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config.yaml
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prefix:
"."
genome_STAR:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines"
lane_ident1:
"_1"
lane_ident2:
"_2"
threads:
12
perl_script_dir:
"/gpfs/project/daric102/circs_hilbert_scratchgs/snakemake_tests/repo_08_03_2021/scripts" # need to sorrect this- might need full parth here
run_name:
"test_srr_2samples"
mm1_script:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/matrixmaker-V4.pl"
mm1_refseq_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/genes_to_refseqID_nc_and_nr.tsv"
mm1_circ_bedfile:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/circbase_known_circs.bed"
mm2_script:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/matrixtwo_V4.pl"
micrornas_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/miRNA_circRNA_ineractions.txt"
circbank_coding_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/circRNA_protein_coding_potential.txt"
hallmarks_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/hallmark_genes.tsv"
ensembl_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/mart_export_ensembl_gene_desc.txt"
mapping_script:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ/read_mapping.pl"
voting_script:
"/gpfs/project/daric102/circs_hilbert_scratchgs/snakemake_tests/circs_snake/scripts/auto_voting_usable_hpc_outputs.R"
normalization_script:
"/gpfs/project/daric102/circs_hilbert_scratchgs/snakemake_tests/circs_snake/scripts/norm_a_voted_circs_df.R"
bowtie2_ref:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/hg19"
fc_scripts_dir:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines"
chrom_fastqs:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/genome/chroms"
annotation_bed:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/Genes_RefSeq_hg19_09.20.2013.bed"
strict:
"0"
perl_scripts:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/auto_find_circ"
python_exec:
"/software/python/2.7.5/ivybridge/bin/python"
bowtie2_exec:
"/software/Bowtie2/2.1.0/ivybridge/bin/bowtie2"
cx_parse_command:
# "python /home/daric102/.local/bin/CIRCexplorer2 parse -t STAR"
"/software/python/2.7.5/ivybridge/bin/python /gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/star_parse.py"
# for cx2: "python /home/daric102/.local/bin/CIRCexplorer2 parse -t STAR"
cx_annotate_command:
# "python /home/daric102/.local/bin/CIRCexplorer2 annotate"
"/software/python/2.7.5/ivybridge/bin/python /gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/CIRCexplorer.py"
refseq_anot_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/hg19_ref.txt"
fasta_ref:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/hg19.fa"
pl_script_dir:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/circexplorer1_auto"
refseq_file_dcc:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/all_ref.gtf"
fasta_reference:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/hg19.fa"
dcc_command:
"/software/python/2.7.5/ivybridge/bin/python /gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/DCC/main.py"
#"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/DCC/main.py"
bed_ref:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/pipelines/Genes_RefSeq_hg19_09.20.2013.bed"
parse_file:
"/gpfs/project/daric102/circs_hilbert_scratchgs/repo/circs/automate_DCC/dcc_outreader.pl"