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View Code? Open in Web Editor NEWScripts and utilities for providing fastqs to workflows
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Error when providing '-m' parameter to fetchFastq.sh on macOS
I noticed that the following works
$ fetchFastq.sh -f ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz -t ERR035229.fastq.gz
however when providing -m wget value it produces an error:
$ fetchFastq.sh -f ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz -t ERR035229.fastq.gz -m wget
Downloading ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz to .../ERR035229.fastq.gz using wget
No such directory ‘vol1/fastq/ERR035/ERR035229’.
gzip: ERR035229.fastq.gz.tmp: unexpected end of file
No such directory ‘vol1/fastq/ERR035/ERR035229’.
gzip: ERR035229.fastq.gz.tmp: unexpected end of file
No such directory ‘vol1/fastq/ERR035/ERR035229’.
gzip: ERR035229.fastq.gz.tmp: unexpected end of file
ERROR: Failed to retrieve ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz to ERR035229.fastq.gz
Failed to download ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz from ena with wget: download failed
`convert_ena_fastq_to_uri` returns URI with double `/` which breaks downloads
This is currently happening because convert_ena_fastq_to_uri calls get_library_path without a second argument (for the root):
producing a leading / which then when concatenated at
//.Retrieval method `wget` should not be passed explicitly to the command
Explicitly passing wget as a retrieval method gives an error:
> fetchEnaLibraryFastqs.sh -l ERR2890000 -d "./" -t fastq -n PAIRED -m wget -s ena -p public
Downloading file ERR2890000_1.fastq.gz for ERR2890000 to /path/to/tmpdir/atlas-fastq-provider
/path/to/atlas-fastq-provider-functions.sh: line 1179: fetch_file_from_ena_over_wget: command not found
fetch_file_from_ena_over_wget method does not exist because the function name is built with the method using fetch_file_from_ena_over_$method. Only fetch_file_from_ena_over_http, fetch_file_from_ena_over_ftp, and fetch_file_from_ena_over_ssh exist (see functions here)
The method wget is implied in some methods, and handled internally by the code.
Remove any indication in readme and usages that wget can be explicitly passed to the command.
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