Problem with miRbase species selection
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Ryan Douglas
Aug 3, 2012, 3:13:09 PM8/3/12
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I just installed SeqBuster on Mac OS X 10.6. When I try to select a species for miRbase under miRNA detection I don't see any species to select from. It looks to be code. Attached is a screenshot of what I'm seeing. Any suggestions for how to fix this?
lorena.pantano
Aug 6, 2012, 3:28:11 AM8/6/12
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Hi,
It os very weird. Do you have the folder DB inside the seqbuster folder, and the file mbhairpinRNA.db inside. Could u check the content of the file? is it fasta file?
cheers
Lorena Pantano
Aug 8, 2012, 3:34:26 AM8/8/12
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Hi,
did you install SeqBuster by svn command? it is weird you have that.
Actually I can not explain it. Just in case, here the instruction to
install it:
svn co http://seqbuster.svn.sourceforge.net/svnroot/seqbuster seqbuster
cd seqbuster
java -jar -Xms2000m -Xmx2000m SeqBuster.jar
And if you did that, the file can be found here:
http://seqbuster.svn.sourceforge.net/viewvc/seqbuster/DB/mbhairpinRNA.db?revision=37
Lo
On Tue, Aug 7, 2012 at 7:42 PM, Ryan Douglas <rndo...@gmail.com> wrote:
> Here's a screenshot of mbhairpinRNA.db. It appears to be an HTML file
> instead of a FASTA. How can I go about getting the proper file?
>
> --
>
>
did you install SeqBuster by svn command? it is weird you have that.
Actually I can not explain it. Just in case, here the instruction to
install it:
svn co http://seqbuster.svn.sourceforge.net/svnroot/seqbuster seqbuster
cd seqbuster
java -jar -Xms2000m -Xmx2000m SeqBuster.jar
And if you did that, the file can be found here:
http://seqbuster.svn.sourceforge.net/viewvc/seqbuster/DB/mbhairpinRNA.db?revision=37
Lo
On Tue, Aug 7, 2012 at 7:42 PM, Ryan Douglas <rndo...@gmail.com> wrote:
> Here's a screenshot of mbhairpinRNA.db. It appears to be an HTML file
> instead of a FASTA. How can I go about getting the proper file?
>
>
>
Ryan Douglas
Aug 8, 2012, 12:40:13 PM8/8/12
to seqb...@googlegroups.com
Pasting over the mbhairpinRNA.db file worked!
Now I have a new problem. Whenever I try 'Do miRNA Analysis' I click through the menus then get an error that sends me to /temp/*.Rout
When I look at the file that the error references they all have the same message at the bottom:
Error in file(file, "r", encoding = encoding) :
cannot open the connection
Calls: source -> source -> file
In addition: Warning message:
In file(file, "r", encoding = encoding) :
cannot open file 'Rscripts/R/db.R': No such file or directory
Execution halted
When I installed SeqBuster everything it needed was detected. Any suggestions on what might be wrong? (Sorry, I have limited computer knowledge!)
Now I have a new problem. Whenever I try 'Do miRNA Analysis' I click through the menus then get an error that sends me to /temp/*.Rout
When I look at the file that the error references they all have the same message at the bottom:
Error in file(file, "r", encoding = encoding) :
cannot open the connection
Calls: source -> source -> file
In addition: Warning message:
In file(file, "r", encoding = encoding) :
cannot open file 'Rscripts/R/db.R': No such file or directory
Execution halted
When I installed SeqBuster everything it needed was detected. Any suggestions on what might be wrong? (Sorry, I have limited computer knowledge!)
Ryan Douglas
Aug 8, 2012, 12:42:54 PM8/8/12
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Also, I think I figured out how I got that HTML-like file instead of the miRbase file.
I went to "Check Update" and then clicked "Check" for "Check DB versions:"
That brings up the message "Do you want to update to version <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
I went to "Check Update" and then clicked "Check" for "Check DB versions:"
That brings up the message "Do you want to update to version <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
Lorena Pantano
Aug 9, 2012, 11:15:56 AM8/9/12
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Good.
ok, this file is created during installation. Could u go to the mysql
conf and check if you connect correctly to mysql?
if so, and the files was not created, you can do it manually, it looks like:
hostname<-"localhost"
username<-"root"
pssw<-"here you put the password if you have it"
dbname<-"seqbuster"
port<-0
when you installed mysql, if you didn't do anything else:
username<-"root"
pssw<-"""
But if you didn't complete all the steps in the installation maybe it
breaks. There was a button in the second windows that pop up the first
time you run it, with the label "create" and during this step is when
this file should be created. I attach you how this windows looks like.
PS: thanks to let me know about that problem. I will fix it.
Lo
On Wed, Aug 8, 2012 at 6:40 PM, Ryan Douglas <rndo...@gmail.com> wrote:
> 'Rscripts/R/db.R
ok, this file is created during installation. Could u go to the mysql
conf and check if you connect correctly to mysql?
if so, and the files was not created, you can do it manually, it looks like:
hostname<-"localhost"
username<-"root"
pssw<-"here you put the password if you have it"
dbname<-"seqbuster"
port<-0
when you installed mysql, if you didn't do anything else:
username<-"root"
pssw<-"""
But if you didn't complete all the steps in the installation maybe it
breaks. There was a button in the second windows that pop up the first
time you run it, with the label "create" and during this step is when
this file should be created. I attach you how this windows looks like.
PS: thanks to let me know about that problem. I will fix it.
Lo
On Wed, Aug 8, 2012 at 6:40 PM, Ryan Douglas <rndo...@gmail.com> wrote:
> 'Rscripts/R/db.R
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