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Published 20 hours ago • verified publisher icon bioperl

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

Open cjfields opened this issue 9 years ago • 1 comments

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 avatar Oct 08 '15 02:10 cjfields

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).

cjfields avatar Oct 08 '15 02:10 cjfields