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# SmallRNA config file -*- conf -*-
pipeline_directory: ${pipeline-directory}
data_sub_directory: ${pipeline-process-directory}
"Model::SmallRNAModel":
schema_class: 'SmallRNA::DB'
connect_info:
- "dbi:Pg:dbname=${database-name};host=${database-host}"
- '${database-user-name}'
- '${database-password}'
programs:
ssaha:
path: /applications/ssaha_v31c_amd64/ssaha_v31c_amd64
process_class: SmallRNA::Process::SSAHASearchProcess
patman:
path: /applications/patman-1.2.1/patman
process_class: SmallRNA::Process::PatmanAlignmentProcess
bwa:
path: /applications/bwa/bwa-0.4.9/bwa
process_class: SmallRNA::Process::BWASearchProcess
samtools:
path: /applications/samtools-svn-trunk/samtools/samtools
srf2fastq:
path: /applications/io_lib-1-12-1/progs/srf2fastq
databases:
root: /data/public_data
organisms:
Arabidopsis_thaliana:
database_files:
genome: arabidopsis/TAIR_8/arabidopsis_genome
genome-tair9: arabidopsis/TAIR_9/arabidopsis_genome
trna: PipelinePublicData/genomic_tRNA_database/genomic_tRNA_database_20080929/Athal-tRNAs.fa
mirbase-hairpin: PipelinePublicData/mirBASE_release_14.0/split/hairpin/Arabidopsis_thaliana.fa
mirbase-mature: PipelinePublicData/mirBASE_release_14.0/split/mature/Arabidopsis_thaliana.fa
mirbase-maturestar: PipelinePublicData/mirBASE_release_14.0/split/maturestar/Arabidopsis_thaliana.fa
mrna: arabidopsis/TAIR_8_cdna/TAIR8_cdna_20080412
c24-genome: arabidopsis/detlef_weigel_c24/C24_Contigs_release_0.1/all.fa
ler-genome: arabidopsis/Landsberg_collection_TAIR_Monsanto_24_02_06/Landsberg_collection_TAIR_Monsanto_24_02_06.fasta
Solanum_lycopersicon:
database_files:
genome-old: tomato/v340/bacs.v340.seq.20081007121008.reformatted
genome: tomato/pre_release_assembly_20091201/S_lycopersicum_scaffolds_20091201.reformatted.fa
ests: tomato/est_sequences/solanum_lycopersicum_mRNA_2008_10_21.seq
concat_ests: tomato/est_sequences/solanum_lycopersicum_mRNA_2008_10_21_concatenated.dna
Carmovirus_turnip_crinkle_virus:
database_files:
genome: TCV/TCV.fa
Oryza_sativa:
database_files:
genome: rice/Oryza_sativa/IRGSP_Build5/nuclear_genome.fasta
Benyvirus_rice_stripe_virus:
database_files:
genome: viruses/Benyvirus/rice_stripe_virus_isolate_Zhejiang.fasta
Chlamydomonas_reinhardtii:
database_files:
genome: chlamydomonas/20090120_chlamy_assembly4/C_reinhardtii.main_genome.scaffolds_plus_unmapped_scaffolds.fasta
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