Re: BUG in ncbi-blast+
- To: Tony Travis <tony.travis@minke-informatics.co.uk>
- Cc: debian-med@lists.debian.org
- Subject: Re: BUG in ncbi-blast+
- From: ucko@debian.org (Aaron M. Ucko)
- Date: Wed, 19 Feb 2020 09:46:29 -0500
- Message-id: <[🔎] udlwo8iab3u.fsf@mit.edu>
- In-reply-to: <7388ce58-bdb1-bb71-e863-8f30c1a2237c@minke-informatics.co.uk> (Tony Travis's message of "Fri, 17 Jan 2020 12:56:06 +0000")
- References: <0245d022-c736-ced5-b924-128da923aff9@minke-informatics.co.uk> <20200117091033.GU5261@an3as.eu> <55cd1027-0c24-5615-e61f-d6fc28cdb68e@minke-informatics.co.uk> <20200117115714.GZ5261@an3as.eu> <7388ce58-bdb1-bb71-e863-8f30c1a2237c@minke-informatics.co.uk>
Tony Travis <tony.travis@minke-informatics.co.uk> writes:
> A unit test would need to know where the deb stores ".ncbirc" and
> strace the execution of "blastn" to make sure the executable finds the
> default config file. If NCBI is unset, it looks for
> "/etc/.ncbirc". However, the default location it is installed to under
> Ubuntu is "/etc/ncbi/.ncbirc".
Right, NCBI's C Toolkit (source package ncbi-tools6, binary packages
including ncbi-data) and C++ Toolkit (the basis for ncbi-blast+) wound
up with different conventional locations for system-wide configuration
files. I've bridged this gap by adding a symlink to the latest
ncbi-data binary package, which hit Debian testing this morning and from
what I gather should automatically make it into the next Ubuntu release.
Sorry you ran into trouble here!
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu
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