Tassel5 Standalone Pipeline: Error Could not load Main Class

[wardah khurshida]

Hi

I am trying to use Tassel standalone (first time) I am using the instructions here: https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel5PipelineCLI.pdf.

I need further clarification about a statement which I don't seem to understand the wording of and how to use it:

"In UNIX, use run_pipeline.pl to execute the pipeline. If you are using a Bash Shell on Windows, youmay need to change the following line to use a ; instead of a :

my $CP = join(":", @fl);

I am using Window 10 and Git Bash I have installed Java 10 version as well. This line I think will solve my error message:

Error: Could not find or load main class net.maizegenetics.tassel.TASSELMainApp
Caused by: java.lang.ClassNotFoundException: net.maizegenetics.tassel.TASSELMainApp

I just don't know how to use it correctly. I have attached a screenshot below.

Thanks for the help!

[Terry Casstevens]

That means to modify that line in start_tassel.pl. I've attached the
modified file

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[Terry Casstevens]

Did you try using the modified script that I attached in the previous email?

On Wed, Jul 11, 2018 at 9:33 PM, wardah khurshida <wkmus...@gmail.com> wrote:
> Hi Tyler
> I have changed ":" ----> ";" but I am getting a bash syntax token error ")"
>
> I typed everything myself but still....

> https://groups.google.com/d/msgid/tassel/58d40d6e-3feb-498e-ae66-2e9df3eee055%40googlegroups.com.

[wardah khurshida]

Hi Terry

I have listed the code as

my $CP = join(";", @fl);

but I get a 'bash: syntax error near unexpected token `('

then I placed quotes around it like this: "my $CP = join(";", @fl);"

but then it does not recognize the command.

On Wednesday, July 4, 2018 at 4:56:02 PM UTC-5, Terry wrote:

[wardah khurshida]

I have a question about that  file: Do I simply copy and paste the modified code into Git Bash or do I have to make my own modifications to the file you sent me?

[Terry Casstevens]

I made the modifications in the attached file. Just replace the file
you have with my attached file.

On Wed, Jul 11, 2018 at 10:59 PM, wardah khurshida

> https://groups.google.com/d/msgid/tassel/cd3fdfe8-2665-4092-a359-9e8cd172f3be%40googlegroups.com.

[wardah]

Got it ! Thanks!

Have a pleasant day!

Wardah Mustahsan

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[wardah khurshida]

Hi Terry

I have a follow up question about the -importGuess function is it normal on Windows that when you put this command in for the Tassel program to flash on my screen for a split second then disappear with no files loaded on Git? Should this function not list all files in the standalone folder?

Do I need to change some script? Please look below.

[Terry Casstevens]

-importGuess is generally used from the command line (run_pipeline.pl)
and requires a file name following it.

Your execution would work if there were a supported file name
following -importGuess

On Fri, Jul 13, 2018 at 12:33 AM, wardah khurshida
<wkmus...@gmail.com> wrote:
> Hi Terry
>
> I have a follow up question about the -importGuess function is it normal on
> Windows that when you put this command in for the Tassel program to flash on
> my screen for a split second then disappear with no files loaded on Git?
> Should this function not list all files in the standalone folder?
>
> Do I need to change some script? Please look below.
>
>

> https://groups.google.com/d/msgid/tassel/23bea4d9-d0ef-46df-9f38-53b5920d91e5%40googlegroups.com.

[wardah]

Can you please give an example? 

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For more options, visit https://groups.google.com/d/optout.

--

[Terry Casstevens]

I recommend...

./start_tassel.pl -Xmx6g

Or if you are trying to load a file during TASSEL GUI startup...

./start_tassel.pl -Xmx6g -importGuess mdp_genotype.hmp.txt

> https://groups.google.com/d/msgid/tassel/CAHAyvgKDVgfuUwvxRaU3rtMb_YkuX17ACiFkjgpSKqT4jSu4vw%40mail.gmail.com.