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googlegenomics / pipelines-api-examples

Examples for the Google Genomics Pipelines API.
BSD 3-Clause "New" or "Revised" License
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test_index.sh error with "curl" command #49

Closed smrgit closed 7 years ago

smrgit commented 7 years ago

not sure if this is a script error or a Cloud Shell error, but when trying to use this script while following one of the tutorial examples (in Cloud Shell), the following command failed:

curl -O ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/pilot3_exon_targetted_GRCh37_bams/data/NA06986/alignment/NA06986.chromMT.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam

the problem may be the combination of curl and an ftp url -- modifying the script or including some comments about other options would be helpful -- eg the file can also be obtained from

http://storage.googleapis.com/genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/pilot3_exon_targetted_GRCh37_bams/data/NA06986/alignment/NA06986.chromMT.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam
mbookman commented 7 years ago

Fixed by https://github.com/googlegenomics/pipelines-api-examples/pull/64