Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 18:5680c31cd031 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 593c33d4de9fd7663766c8463d56e4defd608b04
author galaxytrakr
date Mon, 23 Mar 2026 20:51:03 +0000
parents 9fb80e0392ce
children a4186132e1c4
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17:9fb80e0392ce 18:5680c31cd031
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.17" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.18" 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>
15 mkdir -p sra_cache fastq_out && 15 mkdir -p sra_cache fastq_out &&
16 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache/ && 16 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache/ &&
17 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} && 17 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
18 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq && 18 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
19 #if str($layout) == 'paired' 19 #if str($layout) == 'paired'
20 # Move files directly to the single output datasets
21 mv ./fastq_out/${acc}_1.fastq.gz '$output_r1_single' && 20 mv ./fastq_out/${acc}_1.fastq.gz '$output_r1_single' &&
22 mv ./fastq_out/${acc}_2.fastq.gz '$output_r2_single' 21 mv ./fastq_out/${acc}_2.fastq.gz '$output_r2_single'
23 #else 22 #else
24 mv ./fastq_out/*.fastq.gz '$output_r1_single' 23 mv ./fastq_out/*.fastq.gz '$output_r1_single'
25 #end if 24 #end if