1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
To install this module, cd to the directory that contains this INSTALL
file and type the following:
perl Makefile.PL
make
make test
make install
----------------------------------------------------------------------------
NHGRI::Blastall.pm expects that you have NCBI's blastall binary,
wu-blast binaries, or NCBI's blastcl3 binary installed.
If you do not have it you can download the NCBI binary
for several platforms from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
If you do not have the blastcl3 binary you can either compile the
NCBI toolkit (ftp://ftp.ncbi.nlm.nih.gov/toolbox/) or download the Entrez
binaries from (ftp://ncbi.nlm.nih.gov/entrez/CURRENT/).
WU-BLAST is available from (http://blast.wustl.edu/).
----------------------------------------------------------------------------
Certain methods in NHGRI::Blastall expect to find binaries in your path.
METHOD EXPECTED BINARIES
---------- ---------------------
blastall() blastall
blastcl3() blastcl3
wu_blastall wu-blastn wu-blastp, wu-blastx, wu-tblastn, wu-tblastx
----------------------------------------------------------------------------
If you are using the blastall or wu_blastall methods
you need to make sure the BLASTDB environmental variable is set.
If you stored your BLAST formatted databases in /usr/local/ncbi/blast/db
the command under bash, sh, or ksh would be...
BLASTDB=/usr/local/ncbi/blast/db;
export BLASTDB;
under csh or tcsh it would be
setenv BLASTDB /usr/local/ncbi/blast/db
Also make sure you have a .ncbirc file in your home directory or in
$NCBI/.ncbirc.
---------------------------------------------------------------------------
If you are having problems using the blastall method you may want to test
BLAST from the command line.
cd NHGRI-Blastall-0.xx
blastall -d vector -p blastn -i t/fasta.seq
if this fails than the problem is probably one of the following
a. you don't have the vector database installed
b. you don't have the blastall binary in your path
c. you don't have NCBI's BLAST2.xx installed on your machine
d. the user that you are running the test under does not have
the correct environment settings (see above)
------------------
If you have trouble installing NHGRI::Blastall.pm because you have
insufficient access privileges to add to the perl library directory,
you can still use NHGRI::Blastall.pm. You would want to do something
like:
perl Makefile.PL LIB=~/lib
See perldoc ExtUtils::MakeMaker for more details on this.
If you have problems send mail to: webblaster@nhgri.nih.gov
Read the POD docs in Blastall.pm
try perldoc NHGRI::Blastall
|
