I'm having problems starting Flux-capacitor.

I have the correct java RunTim env: 

C:\>java -version

java version "1.6.0_20"
Java (TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode)
When I launch the wrapper script:
>flux-capacitor.bat -t capacitor

I get "cant find tool capacitor".
I can access the help files etc.
Can any one give me a hand on this?
I'm looking to process the Geuvadis data set BAM files from ArrayExpress - although I have sliced the files with samtools.
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5 Comments

  1. Thasso Griebel

    Hi Chris,

    there are a couple of things you can try:

    1) Try to run the capacitor without explicitly specifying a tool. The capacitor should be the default tool.

    2) If you run "flux-capacitor.bat --help", the end of the output should contain a list of tools. Which tools are listed there ?

    3) Run all commands with "–log DEBUG" and copy the output here so we can take a look and figure out what is going on. 

    Finally, from what you wrote I figure you are on Windows ? Which versions of Windows and the Capacitor are you running ?

    Best,

    -Thasso

  2. Chris Odhams

    Hi Thasso,

     

    Thanks for getting back to me so quickly!

    I'm using flux-capacitor-1.5.2.

    Windows 7 Professional 64-bit OS. 8GB RAM. 

    1) When I run without a tool I get: "No tools specified, use -t <tool> to specify a tool"

    2) When I run help, I get the help output, then under "List of available tools", there is nothing. 

    3) I can't seem to get any debug outputs. When I run: flux-capacitor.bat -t capacitor -log DEBUG. I get the same output as normal "Flux-capacitor v1.5.2 <Flux Library: 1.27>

    capacitor tool not found"

     

    Any ideas?

    BW,

    Chris

    1. Thasso Griebel

      Hmm, sounds to me like we have an issue with the .bat start script on windows. I created a ticket ( BARNA-364 - Getting issue details... STATUS ) and added you to the watch list so you will receive emails from the JIRA when we work on this. Give me a little bit of time as I have to find a Windows Machine where I can test this (smile)

    2. Thasso Griebel

      Hey Chris,

      sorry, it took a moment to get hands on a Windows machine. I could reproduce the problem and, at least for me, it was related to spaces in the path name to the capacitor. When I copied the capacitor to C:\ to make sure there are no spaces in the path, it worked and all tools were detected correctly. I have to look more closely to figure out the reasons, but I hope that works around the issue for now and you can get it to work

      Cheers,

      -Thasso

       

  3. Chris Odhams

    Hi Thasso,

     

    I changed the path to D:\ with no spaces - works fine!

    Thank you very much!