Java.io.EOFException: Unexpected end of ZLIB input stream
Hi guys.
I am trying to unzip a file (a zipped directory from a remote server) using the 'jar xvf' command. The problem is, it extracts a few of the items therein and throws the below error message:
Has anyone else come across this issue? How did you fix it.
what do u mean by " 'end of file' unexpected "?
i am running a script called "s1" which internally calls "s2"
now s1 starts running & at a point (where it is suppose to call "s2")
i get a message
'end of file' unexpected....
& my script(s) are not working..
any ideas on this?
regards... (4 Replies)
Hi there again,
Running Solaris 10 with built-in Java. Seems to compile and run fine.
Problem is: Say I want to see contents of current directory. In a shell, I'd just write "ls" and it outputs the content.
When I write a Java file, I have the following line:
System.out.println("ls");
... (1 Reply)
This is the script
path=/oracle/ora10gdb/sample
archive=/oracle/ora10gdb/archive
cd $path
for i in `ls`;do
mv $i $archive
Done
Please tell me why it is givind this error (2 Replies)
HI,
I was converting a .bat file to .sh file for unix
Code snippet
#!/usr/bin/sh
set -x
if then
goto RegularBuild;
CURDIR="$1";
cd "$CURDIR";
:RegularBuild
echo "Checking for existing fip_help.properties in def/properties directory..."
if then
rm -f fip_help.properties;
... (1 Reply)
HELP PLEASE!!
I am running this script, and i keep getting the error 'end of file' unexpected. I know that usually means parenthesis or whatever is out of place but i cant find anything!! I am new to scripting and i put some "print" staements in and it is not getting past the first IF statment... (7 Replies)
Hello Everyone,
The situation is:
$ alias rm="sh abc.sh"
#abc.sh:
read input
echo "The input was: " $input
$ rm xyz.txt
should return
"The input was: xyz.txt"
Here, I want the alias "rm" to execute the file "abc.sh", where "abc.sh" should take "xyz.txt"... (1 Reply)
Hi,
On adding below code to my script shows the error on executing else script works fine.
sqlplus $user_name/$password <<EOL
truncate table order;
commit;
truncate table order_hist;
commit;
insert into order(ID,TRAN,CUST_NAME,OPT_VAL) select * from order_bkp;
insert into... (5 Replies)
I dont know where I missed the double quotes .:wall:pls review this code and help me out .
m1: line 26: unexpected EOF while looking for matching `"'
m1: line 34: syntax error: unexpected end of file
echo "script is created by prabhu Kumar ";
echo "changing the directory to wes... (2 Replies)
Hi,
Need some help with creating a file from input steam. Meaning from following command myfunc should be able to store the input stream to a file.
echo a b c | myfunc
The file thus created should have -
a
b
c
Here's what I've tried in myfunc() but didn't help -
myfunc() { cat... (3 Replies)
Discussion started by: nexional
3 Replies
LEARN ABOUT DEBIAN
bio::tools::run::eponine
Bio::Tools::Run::Eponine(3pm) User Contributed Perl Documentation Bio::Tools::Run::Eponine(3pm)NAME
Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor
SYNOPSIS
use Bio::Tools::Run::Eponine;
use strict;
my $seq = "/data/seq.fa";
my $threshold = "0.999";
my @params = ( '-seq' => $seq,
'-threshold' => $threshold,
'-epojar' => '/usr/local/bin/eponine-scan.jar',
'-java' => '/usr/local/bin/java');
my $factory = Bio::Tools::Run::Eponine->new(@params);
# run eponine against fasta
my $r = $factory->run($seq);
my $parser = Bio::Tools::Eponine->new($r);
while (my $feat = $parser->next_prediction){
#$feat contains array of SeqFeature
foreach my $orf($feat){
print $orf->seqname. "
";
}
}
# Various additional options and input formats are available. See
# the DESCRIPTION section for details.
DESCRIPTION
wrapper for eponine, a mammalian TSS predictor.
The environment variable EPONINEDIR must be set to point at either the directory which contains eponine-scan.jar or directly at the jar
which eponine-scan classfiles. NOTE: EPONINEDIR must point at the real file not a symlink.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR
Email gisoht@nus.edu.sg
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
java
Title : java
Usage : $obj->java('/usr/opt/java130/bin/java');
Function: Get/set method for the location of java VM
Args : File path (optional)
epojar
Title : epojar
Usage : $obj->epojar('/some/path/to/eponine-scan.jar');
Function: Get/set method for the location of the eponine-scan executable JAR
Args : Path (optional)
threshold
Title : threshold
Usage : my $threshold = $self->threshold
Function: Get/Set the threshold for Eponine
Returns : string
Args : b/w 0.9 and 1.0
run
Title : run
Usage : my @genes = $self->run($seq)
Function: runs Eponine and creates an array of features
Returns : An Array of SeqFeatures
Args : A Bio::PrimarySeqI
predict_TSS
Title : predict_TSS
Usage : Alias for run()
_setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: writes input sequence to file and return the file name
Example :
Returns : string
Args :
_run_eponine
Title : run_eponine
Usage : $obj->_run_eponine()
Function: execs the Java VM to run eponine
Returns : none
Args : none
perl v5.12.3 2011-06-18 Bio::Tools::Run::Eponine(3pm)