Closed AleMadLei closed 4 years ago
I have an automated script that tries to download this the resource at "https://www.ebi.ac.uk/ena/data/warehouse/filereport?result=read_run&fields=run_accession,fastq_ftp,fastq_md5&accession=SRR8555091" by calling the script like Scripts/SRA.download.bash SRR8555091 test
Scripts/SRA.download.bash SRR8555091 test
However, this returns a 301 redirection which causes curl to end without receiving any content (thus failing the execution of my script).
There are 2 different ways that this can be addressed.
https://www.ebi.ac.uk/ena/data/warehouse/filereport
https://www.ebi.ac.uk/ena/portal/api/filereport
-L
curl
curl -Ls "$DATA_LINK?$DATA_OPS&accession=$SRX" -o "$DIR/srr_list.txt"
I've created the following PR to address this https://github.com/lmrodriguezr/enveomics/pull/47
I have an automated script that tries to download this the resource at "https://www.ebi.ac.uk/ena/data/warehouse/filereport?result=read_run&fields=run_accession,fastq_ftp,fastq_md5&accession=SRR8555091" by calling the script like
Scripts/SRA.download.bash SRR8555091 test
However, this returns a 301 redirection which causes curl to end without receiving any content (thus failing the execution of my script).
There are 2 different ways that this can be addressed.
https://www.ebi.ac.uk/ena/data/warehouse/filereport
tohttps://www.ebi.ac.uk/ena/portal/api/filereport
-L
option to thecurl
call so that it follows redirects. Line would becurl -Ls "$DATA_LINK?$DATA_OPS&accession=$SRX" -o "$DIR/srr_list.txt"