"getAbsPath"? Attempting to run Birdsuite
Hi again,
This forum was very helpful in answering my previous question about scripting, so I'm going to try again with another problem that I have been having for a couple weeks now (the software support have not replied to my questions, unfortunately). In brief: I am trying to run Birdsuite (64-bit version: http://www.broadinstitute.org/scienc...dsuite-install). I followed the installation instructions exactly and attempted to run the test code at the bottom of the installation web page. The commands I used are the following: Code:
/home2/jason/EXEDIR/birdsuite.sh --basename=test --exeDir=/home2/jason/EXEDIR/ --metadataDir=/home2/jason/EXEDIR/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=/home2/jason/EXEDIR/TESTDIR/test.gender --celFiles=/home2/jason/EXEDIR/TESTDIR/test.cels --noLsf --apt_probeset_summarize.force --outputDir=/home2/jason/EXEDIR/TESTDIR/TEST_OUT/ More information about the invocation commands/options here: http://www.broadinstitute.org/scienc...ite/invocation -------------------------------- Unfortunately, when attempting to run the above, I get this error in the log: Quote:
Here's the code to "birdsuite.sh", the relevant "line 40" from the error is bolded: Code:
#! /bin/bash What exactly is this "getAbsPath" file or directory from the above code? Is it a necessary component? How would I tweak the shell script to get this working? I am very confused. Sorry for asking these stupid questions. Thank you very much for your help! |
According to the code you should have an executable in your exedir called getAbsPath.
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of the script where it refers to $exedir |
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I would think where you are getting the birdsuite software from should tell you which version of java you require and any other associated files / apps.
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I am also stuck at the same step as you. Did you manage to get "getAbspath" somewhere? If so, could you please tell me where? or could you send it to me? Thanks in advance |
Hi chariko,
You can download getAbsPath here: http://sourceforge.net/projects/getabspath/ Extract and compile to your EXEDIR folder. Interestingly, when I reinstalled Birdsuite, getAbsPath was present. Not sure what I did incorrectly the first time around. Unfortunately, I'm running into a bunch of other errors that I'm slowly solving one by one... if you run into issues, please feel free to post here/pm me, hopefully we can help each other out. :) Thanks. |
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