bioperl/bioperl-run

ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail

cjfields opened this issue · 1 comments

cjfields commented

Author Name: Joel Martin (Joel Martin)
Original Redmine Issue: 2908, https://redmine.open-bio.org/issues/2908
Original Date: 2009-09-01
Original Assignee: Bioperl Guts

ecoli.nt is no longer in ftp://ftp.ncbi.nih.gov/blast/db/FASTA
without this a number of tests in t/Tools/Run/StandAloneBlast.t are skipped, then tests 43 fails as the sequence it needs wasn’t read due to the skipped tests ( would have been read in ->next_seq if they hadn’t been skipped ).

seems recent that ecoli.nt quit existing as this test passed for me recently.
or we’ve just had a recent resync with ncbi.

cjfields commented

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2009-09-01T08:43:03Z

These tests aren’t normally run anyway (it requires an optional BLAST installation), so the issue is minor. Should be easy enough to correct within the toolkit (maybe use something that’s already present).