run bin/prepare-refseqs.pl outside of JBrowse root dir #465

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chienchi opened this Issue Apr 10, 2014 · 4 comments

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Can't locate local/lib.pm in @inc (@inc contains: extlib/lib/perl5 /home/chienchi/JBrowse-1.11.3/bin/../src/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /home/chienchi/JBrowse-1.11.3/bin/../src/perl5/JBlibs.pm line 24.

If I added a dollar sign($) before extlib at JBlibs.pm line 24, the issue is fixed.
* lib->import( "$extlib/lib/perl5" );

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cmdcolin Apr 10, 2014

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I just tested it (forgot the double quotes to expand the $extlib var at first) and it looks good. Thanks for the fix!

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cmdcolin commented Apr 10, 2014

I just tested it (forgot the double quotes to expand the $extlib var at first) and it looks good. Thanks for the fix!

@cmdcolin cmdcolin closed this in 9a505e2 Apr 10, 2014

@cmdcolin cmdcolin added this to the Release 1.11.4 milestone Apr 10, 2014

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rbuels Apr 10, 2014

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This does not look right.
On Apr 10, 2014 3:00 PM, "Colin" notifications@github.com wrote:

Closed #465 #465 via 9a505e29a505e2
.

Reply to this email directly or view it on GitHubhttps://github.com/GMOD/jbrowse/issues/465
.

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rbuels commented Apr 10, 2014

This does not look right.
On Apr 10, 2014 3:00 PM, "Colin" notifications@github.com wrote:

Closed #465 #465 via 9a505e29a505e2
.

Reply to this email directly or view it on GitHubhttps://github.com/GMOD/jbrowse/issues/465
.

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cmdcolin Apr 10, 2014

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@rbuels it looks a little weird but I think the relative paths resolve themselves to make it work. the full path of extlib when it runs is like "full_path_to_/jbrowse/bin/../src/perl5/../../extlib" (<-- edit to include full path)

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cmdcolin commented Apr 10, 2014

@rbuels it looks a little weird but I think the relative paths resolve themselves to make it work. the full path of extlib when it runs is like "full_path_to_/jbrowse/bin/../src/perl5/../../extlib" (<-- edit to include full path)

cmdcolin added a commit that referenced this issue May 7, 2014

Add configurable highResolutionMode parameter that can be 'auto' or '…
…disabled' or a custom ratio. Adds a getResolution method to Util.js. Clean up references to the devicePixelRatio in other code. See issue #465
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cmdcolin May 7, 2014

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I referenced the wrong issue number in the above commit (sorry) see issue #456

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cmdcolin commented May 7, 2014

I referenced the wrong issue number in the above commit (sorry) see issue #456

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