IGV release 2.3.60 -- important change to session files

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Jim Robinson

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Sep 21, 2015, 7:19:42 PM9/21/15
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Hi,  IGV 2.3.60 was just released with an important change to the treatment of paths in session files.  By default all paths are now written in "absolute" form.  To enable generation of relative paths you need to check a new user preference under the General category,   "Use relative paths in session files."    This change was made due to some intractable errors in relative path computation in situations involving certain Linux/Java combinations and symbolic links.    If you are not experiencing these problems and prefer to keep using relative paths please select the user preference   (View > Preferences > General).

Jim

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Malcolm Cook

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Nov 27, 2015, 7:46:00 PM11/27/15
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OK, 

Q1: Should I expect relative paths to work when a session is opened by URL?  

Q2: Should I expect to still have to set relativePath="true" on Resource elements in my session file, as documented in the release note:

IGV 1.5.30, released October 2010

  • Relative file paths can now be used in session XML files.  If the "relativePath" attribute of a Resource element is set to true the resource file path will be interpreted relative to the location of the session file.  Note: if relativePath is used the corresponding "Track" elements, if any, for the file will be ignored. 
Thanks,

Malcolm

Jim Robinson

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Nov 27, 2015, 8:52:05 PM11/27/15
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Yes, you should expect relative paths to work.  You do not need to set the relativePath attribute.
OK, 

Should I expect relative paths to work when a session is opened by URL?  Also, I seem to remember that 

Should I expect to still have to set relativePath="true" on Resource elements in my session file, as documented in the following:

IGV 1.5.30, released October 2010

  • Relative file paths can now be used in session XML files.  If the "relativePath" attribute of a Resource element is set to true the resource file path will be interpreted relative to the location of the session file.  Note: if relativePath is used the corresponding "Track" elements, if any, for the file will be ignored. 
Thanks,

Malcolm

On Monday, September 21, 2015 at 6:19:42 PM UTC-5, Jim Robinson wrote:
Hi,  IGV 2.3.60 was just released with an important change to the treatment of paths in session files.  By default all paths are now written in "absolute" form.  To enable generation of relative paths you need to check a new user preference under the General category,   "Use relative paths in session files."    This change was made due to some intractable errors in relative path computation in situations involving certain Linux/Java combinations and symbolic links.    If you are not experiencing these problems and prefer to keep using relative paths please select the user preference   (View > Preferences > General).

Jim

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Jim Robinson

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Nov 27, 2015, 8:53:58 PM11/27/15
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Yes re Q1,  no re Q2.   The change in 2.3.60 affects how they are written, not read.   You can still force IGV to try to write relative paths, with the user preference as noted, but by default it will use absolute.


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