Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 19:a4186132e1c4 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit ba119cea4881b4ff3a27470d8b426902977290b3
author galaxytrakr
date Mon, 23 Mar 2026 22:01:24 +0000
parents 5680c31cd031
children 2b4efa539c71
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18:5680c31cd031 19:a4186132e1c4
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.18" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.19" profile="23.0">
2 <description>Fetches SRA runs from AWS and converts them to FASTQ</description> 2 <description>Fetches SRA runs from AWS and converts them to FASTQ</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.34.8">awscli</requirement> 4 <requirement type="package" version="2.34.8">awscli</requirement>
5 <requirement type="package" version="3.2.1">sra-tools</requirement> 5 <requirement type="package" version="3.2.1">sra-tools</requirement>
6 <requirement type="package" version="2.8">pigz</requirement> 6 <requirement type="package" version="2.8">pigz</requirement>
31 echo "Processing batch accession: $acc" && 31 echo "Processing batch accession: $acc" &&
32 mkdir -p sra_cache_${acc} fastq_out_${acc} && 32 mkdir -p sra_cache_${acc} fastq_out_${acc} &&
33 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ && 33 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ &&
34 fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} && 34 fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} &&
35 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq && 35 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq &&
36 #if str($layout) == 'paired' 36 (
37 # Move files to the special path for collection discovery 37 #if str($layout) == 'paired'
38 mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' && 38 mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' &&
39 mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz' 39 mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz'
40 #else 40 #else
41 mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz' 41 mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz'
42 #end if && 42 #end if
43 ) &&
43 rm -rf sra_cache_${acc} fastq_out_${acc} 44 rm -rf sra_cache_${acc} fastq_out_${acc}
44 #end if 45 #end if
45 #end for 46 #end for
46 #end if 47 #end if
47 ]]></command> 48 ]]></command>