# Unable to download and extract Reads from NCBI SRA on local Galaxy

**URL:** <https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759>\
**Category:** Uncategorized\
**Tags:** download, sra\
**Created:** [March 27, 2022, 3:56am UTC](https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759 "2022-03-27T03:56:44Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Marika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marika/32/3239_2.png) [@Marika](https://help.galaxyproject.org/u/Marika)\
**Post date:** [March 27, 2022, 3:56am UTC](https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759/1 "2022-03-27T03:56:44Z")

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Hi,  
I am unable to download and extract Reads from NCBI SRA on local Galaxy . I installed the sra tolls from the tool shed. I gave me 3 tools: download and extract Reads from NCBI SRA on local Galaxy in BAM ,FASTQ and FASTA/Q format. I tried both FASTQ and FASTA/Q tools. Every time I get the same error : _condition violated while updating node - Warning: normally this application should not be run as root/superuser._  
I found a small message in red in the install page saying the this tool need API authentication. ( I am not sure 100% from the terminology, the page disappeared when I clicked on the tool)

I am not sure if I must configure the tool itself. I tried the job as normal user and as admin also using an accession list and one accession only…  
Can you help me please? or suggest any other way to download 122 runs from SRA NCBI?  
Thank you in advance.

I am able to run this tool on the org server, but the problem that I need to use 2 other tools that are not on the org server ( IsoRead and armDB) that’s why I decided to have a local galaxy.

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**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [March 28, 2022, 12:46am UTC](https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759/2 "2022-03-28T00:46:21Z")

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Hi @Marika,  
you can try upload using URLs. While this option requires manual cut and past, on some servers it is significantly faster than the dedicated importer tools. Both NCBI and ENA provide links to fastq(.gz) files. Copy and past link into Galaxy Upload menu \> Paste/Fetch data section. At least you can start data analysis.  
Kind regards,  
Igor

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [May 8, 2024, 7:58pm UTC](https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759/3 "2024-05-08T19:58:01Z")

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A post was split to a new topic: [Configuring download and extract Reads from NCBI SRA on local Galaxy](https://help.galaxyproject.org/t/configuring-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/12450)

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [May 8, 2024, 7:58pm UTC](https://help.galaxyproject.org/t/unable-to-download-and-extract-reads-from-ncbi-sra-on-local-galaxy/7759/4 "2024-05-08T19:58:12Z")

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