Mercurial > repos > iuc > sra_tools
changeset 24:e08a7ad4378b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
| author | iuc |
|---|---|
| date | Mon, 01 Feb 2021 20:03:42 +0000 |
| parents | 653e89d73fc4 |
| children | 69ebb7f46e45 |
| files | fasterq_dump.xml sra_macros.xml test-data/SRR11859153.fastq.gz |
| diffstat | 3 files changed, 21 insertions(+), 4 deletions(-) [+] |
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--- a/fasterq_dump.xml Thu Aug 20 05:06:27 2020 -0400 +++ b/fasterq_dump.xml Mon Feb 01 20:03:42 2021 +0000 @@ -14,13 +14,16 @@ ln -s '${input.file}' "\$acc" && #end if @CONFIGURE_RETRY@ + ## fetch from public s3 bucket if we can + export acc_or_path="\$acc" && + aws s3 cp --no-sign-request "s3://sra-pub-sars-cov2/run/\$acc/\$acc" "\$acc.sra" 2>&1 | tee '$log' && export acc_or_path="\$acc.sra"|| true && while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do - fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} + fasterq-dump "\$acc_or_path" -e \${GALAXY_SLOTS:-1} $adv.split #if str( $adv.minlen ) != "": --min-read-len "$adv.minlen" #end if - $adv.skip_technical 2>&1 | tee $log; + $adv.skip_technical 2>&1 | tee -a '$log'; if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then break ; else @@ -192,6 +195,19 @@ </element> </output_collection> </test> + <test> + <!-- test accession downloaded from public bucket --> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR11859153"/> + <output_collection name="output_collection" type="list"> + <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/> + </output_collection> + <output name="log"> + <assert_contents> + <has_text text="download: s3://sra-pub-sars-cov2/"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does?**
--- a/sra_macros.xml Thu Aug 20 05:06:27 2020 -0400 +++ b/sra_macros.xml Mon Feb 01 20:03:42 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.10.8</token> + <token name="@VERSION@">2.10.9</token> <token name="@ACCESSIONS_FROM_FILE@"> grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' </token> @@ -35,7 +35,8 @@ <macro name="requirements"> <requirements> <requirement type="package" version="@VERSION@">sra-tools</requirement> - <requirement type="package" version="2.3.4">pigz</requirement> + <requirement type="package" version="1.18.222">awscli</requirement> + <requirement type="package" version="2.5">pigz</requirement> <yield/> </requirements> </macro>