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.