Trying to get tassel pipeline installed on Windows 7 (64) to run GBS pipeline

[Lucinda]

Hi everyone,
I am just trying to get my GBS pipeline running using tassel, and I have an error in the class path (I think). I downloaded Tassel 3.0 Standalone today (12/17/2012). I'm not very used to working with PCs, which is maybe my problem here... (ps. I have java 1.7.0_10 64bit if that matters).

I entered:  "C:\Program Files (x86)\tassel\run_pipeline.bat" -fork1 FastqToTagCountPlugin -i qseq -k attachment1.txt -e EcoT22I -o tagCounts -endPlugin -runfork1

(I dragged and dropped the .bat file for execution).

I get the result "Error: Could not find of load main class net. maizegenetics.pipeline.TasselPipeline"

I went and looked in my run_pipeline file, and this is what it says (I upgraded the memory a little since the machine has 16g of ram):

@echo off

set TOP=.
set LIB_JARS=%TOP%\lib

set CP=%TOP%\sTASSEL.jar
for %%i in (%LIB_JARS%\*.jar) do call "%TOP%\cp.bat" %%i
echo %CP%

java -classpath "%CP%" -Xms512m -Xmx6g net.maizegenetics.pipeline.TasselPipeline %*


Thanks so much for any help in figuring this out.

[Terry Casstevens]

Hi, Lucinda,

You need to define TOP to be your installation directory. The perl
version run_pipeline.pl doesn't need that modification.

Cheers,

Terry

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[Lucinda]

Thanks Terry,
Just to clarify, I should delete the . that is there currently and put C:\Program Files (x86)\tassel  there instead?
Thanks!
-Lucinda

[Terry Casstevens]

Yes

> https://groups.google.com/d/msg/tassel/-/HA1n90SH6KMJ.

[Lucinda]

So, now my .bat file says:
set TOP=C:\Program Files (x86)\tassel (for both run_pipeline.bat and start_tassel.bat"

Something isn't quite right about that.

the new error says "\tassel\lib*.jar was unexpected at this time"
and start_tassel.bat doesn't open when I double click on it anymore.

This is definitely just the renamed tassel3.0 folder, so I don't think that I could have the path wrong. Maybe it doesn't like the spaces?

Any more ideas?
Thanks!
-Lucinda

[Terry Casstevens]

Try putting it in quotation marks since you have a space in the directory name.

set TOP="C:\Program Files (x86)\tassel"

> https://groups.google.com/d/msg/tassel/-/UQqkpp8br_kJ.

[Lucinda]

I've been messing around with options like that. In quotes, it outputs: '""C:\Program' is not recognized as an internal or external command, operable program or batch file. About 40 times (I didn't really count, but it's more than 20). All quotes are output, not ones that I added.

Then it ends with "C:\Program Files (x86)\tassel"\sTassel.jar
Error: Could not find or load main class Files

Maybe this is because I specified the whole path for the .bat file, and then specify the whole path within the .bat file? It seems to be seeing a lot of quotes...

[Lucinda]

backwards slashes for the spaces don't help either.

[Jorge Mauricio Gonzalez Campos]

Lucinda 

I have the same problem? you solved it ? 

[maria.da...@gmail.com]

Hello, Jorge. Did you solve the problem? I'm having the exact same problem.

[Terry Casstevens]

Please see the last trouble shooting item

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ExecutingTassel.pdf

And also considering using bash shell via cygwin on Windows

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