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install.sh Issues #6

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definitivequestion opened this issue Feb 21, 2020 · 0 comments

definitivequestion commented Feb 21, 2020

The following lines in the install.sh script need to be changed to account for changes in the upstream server structure.

This is the broken line.

curl -o external_data/genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai

This is the replacement line

curl -o external_data/genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai

Here is another broken line

curl -o external_data/genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

Here is a possible replacement.

curl -o external_data/genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

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