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From: Brian H. <bh...@br...> - 2014-06-06 16:46:12
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Hi Joel, I'm wondering if we already resolve this issue in our development code, as it's changed from the version you're using. If you want to give it a try, you can pull it like so: svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk transdecoder-code-0 best, ~brian On Fri, Jun 6, 2014 at 11:34 AM, Joel Fillon, Mr <joe...@mc...> wrote: > Hi Brian, > > When I rerun transdecoder in a directory where it was already run, I get > an error during symlink creation: > ln: creating symbolic link `Trinity.fasta.transdecoder.pfam.dat.domtbl': > File exists > > Not a big deal; I can delete the symlink first but maybe you could do it > in the same way you overwrite other files. > > I guess it's in: > > trinityrnaseq_r20140413p1/trinity-plugins/TransDecoder_r20131110/ > pfam_runner.pl > > lines 183 and 210: replace > > &process_cmd("ln -s $pfam_out $pfam_out.domtbl"); > > by > > &process_cmd("ln -s -f $pfam_out $pfam_out.domtbl"); > > Thanks for your work! > Best > Joël > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > _______________________________________________ > Transdecoder-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transdecoder-users > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
