[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>> </FONT></SPAN>i set "mpiblast.conf" as
follow<BR>>/home/ct/toolkit/mpiBLAST-1.0.1<BR>>/home/ct/toolkit/mpiBLAST-1.0.1<BR>>/home/ct/toolkit/ncbi/bin<BR><SPAN
class=542491413-14052003><FONT face=Arial color=#0000ff size=2>[Osborne,
John] </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> storage location. You don't want to have your ncbi directory
in there at all. 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> </DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff
size=2>According to the readme, this file should contain 3 lines. 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> </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> </DIV>
<DIV><SPAN class=542491413-14052003><FONT face=Arial color=#0000ff size=2>Hope
this helps. 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> </DIV>
<DIV><SPAN class=542491413-14052003> <FONT face=Arial color=#0000ff size=2>
-John</FONT></SPAN></DIV>
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