search

cbuhay / ExCID

The Exome Coverage and Identification Report displays the coverage of every target region in your capture design. It also displays regions below an adjustable coverage threshold.
14 stars 5 forks source link

ExCID.grep_gene_list_pct_Final-miRNA.pl and ExCID.grep_gene_list_pct_Final.pl ignore Config.txt and expect databases to be in $script_dir/database/ #5

Open bpow opened 9 years ago

bpow commented 9 years ago

I'm guessing y'all keep your DataBaseDir in Config.txt set to a subdirectory called database under the ExCID install directory. setup.sh and update_databases.sh will happily put the processed reference files elsewhere if specified by DataBaseDir. However, if you do this, you will get cryptic errors like:

grep: /full/path/to-excid/ExCID/ExCID_v2.0///database/HGMD_2014_v4.bed: No such file or directory

I believe this is because the scripts ExCID.grep_gene_list_pct_Final-miRNA.pl and ExCID.grep_gene_list_pct_Final.pl are expecting HGMD_2014_v4.bed to be in $script_dir/database.

Rashesh7 commented 9 years ago

Thank you for your feedback. This is surely an erroneous assumption. We will address this issue.

Thank you.