[Bioclusters] [mpiBLAST]how to "mpiformatdb nr"

Osborne, John bioclusters@bioinformatics.org
Wed, 14 May 2003 09:21:32 -0400


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> i set "mpiblast.conf" as follow
>/home/ct/toolkit/mpiBLAST-1.0.1
>/home/ct/toolkit/mpiBLAST-1.0.1
>/home/ct/toolkit/ncbi/bin
[Osborne, John] 
This isn't correct, you need to set up a shared storage location (on an NFS
mount or whatever) and a local
 storage location.  You don't want to have your ncbi directory in there at
all.  Mine looks something like this:
/scratch/storage/shared
/scratch/storage/mpiblast_local
 
According to the readme, this file should contain 3 lines.  I think this is
either a typo or the last line
is a blank line (I put a blank line in mine).
 
Your .ncbirc file should have the location of your blast data directory.
 
Hope this helps.  I am going to devote the rest of my morning to getting
mpiblast to run properly, so feel free
to email this list.
 
  -John
 

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<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>&gt;&nbsp;</FONT></SPAN>i set "mpiblast.conf" as 
follow<BR>&gt;/home/ct/toolkit/mpiBLAST-1.0.1<BR>&gt;/home/ct/toolkit/mpiBLAST-1.0.1<BR>&gt;/home/ct/toolkit/ncbi/bin<BR><SPAN 
class=542491413-14052003><FONT face=Arial color=#0000ff size=2>[Osborne, 
John]&nbsp;</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>This 
isn't correct, you need to set up a shared storage location (on an NFS mount or 
</FONT></SPAN><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>whatever) and a local</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>&nbsp;storage location.&nbsp; You don't want to have your ncbi directory 
in there at all.&nbsp; Mine looks </FONT></SPAN><SPAN 
class=542491413-14052003><FONT face=Arial color=#0000ff size=2>something like 
this:</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>/scratch/storage/shared</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>/scratch/storage/mpiblast_local</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2>According to the readme, this file should contain 3 lines.&nbsp; I think 
this is either a typo or the last line</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>is a 
blank line (I put a blank line in mine).</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>Your 
.ncbirc file should have the location of your blast data 
directory.</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>Hope 
this helps.&nbsp; I am going to devote the rest of my morning to getting 
mpiblast to run properly, so feel free</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>to 
email this list.</FONT></SPAN></DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff 
size=2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=542491413-14052003>&nbsp;<FONT face=Arial color=#0000ff size=2> 
-John</FONT></SPAN></DIV>
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