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Bug 295584 - sci-biology/ncbi-tools: hardcoded path to seg(1) is wrong
Summary: sci-biology/ncbi-tools: hardcoded path to seg(1) is wrong
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2009-12-03 20:04 UTC by Martin Mokrejš
Modified: 2013-02-17 10:15 UTC (History)
0 users

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Package list:
Runtime testing required: ---


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Description Martin Mokrejš 2009-12-03 20:04:03 UTC
It seems to me seg-based filtering or low-complexity regions in BLAST cannot work. I see using:

$ strings /usr/bin/blastpgp | less
[cut]
BLASTFILTER
seg 
%s%s%s%s%s
/usr/ncbi/blast/filter
Call to seg failed.
^z
$ ls -la /usr/ncbi/blast/filter
ls: cannot access /usr/ncbi/blast/filter: No such file or directory
$ ls -la /usr/share/ncbi             
total 16
drwxr-xr-x   4 root root 4096 Apr 18  2008 .
drwxr-xr-x 139 root root 4096 Dec  2 03:56 ..
drwxr-xr-x   2 root root 4096 Dec  2 02:03 data
drwxr-xr-x   2 root root 4096 Apr 18  2008 formatdb
$
Comment 1 Martin Mokrejš 2009-12-03 20:41:01 UTC
(In reply to comment #0)
> It seems to me seg-based filtering or low-complexity regions in BLAST cannot
                         ------------of (was a typo, sorry)
> work. I see using:
Comment 2 Justin Lecher gentoo-dev 2013-02-17 09:55:00 UTC
So what should we do here? There are no filter installed. What does upstream intend? Do one need to download them seperately?