search

bioperl / bioperl-live-redmine

Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
0 stars 0 forks source link

ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail #59

Open cjfields opened 8 years ago

cjfields commented 8 years ago

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 8 years ago

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).