Question: Why The Result Files Are Empty ? And Is Java Applet Supported By Galaxy System?
gravatar for liyanhui607
7.3 years ago by
liyanhui60720 wrote:
Hi All, We want to add a program Ą°PhyML 3.0Ąą to galaxy system. This software was for phylogenetic developed byhttp://www.atgc- can run normally in Linux environment with a file for example named Ą°sampleĄą as input and two files automatically named Ą°sample.phy_phyml_stats.txtĄą and Ą°sample.phy_phyml_tree.txtĄą as outputs. However, after added it to galaxy system, we found that it can produce the right result files in directory "/var/we/galaxy- dist/database/files/000Ąą, but they did not return to the web page where they are empty. So who can tell me what is wrong? Another question, is java applet supported by galaxy system? Thank you very much! Best Wishes! Yan-Hui Li
galaxy • 924 views
ADD COMMENTlink modified 7.3 years ago by Jelle Scholtalbers360 • written 7.3 years ago by liyanhui60720
gravatar for Jelle Scholtalbers
7.3 years ago by
Jelle Scholtalbers360 wrote:
Dear Yan-Hui Li, you have to make sure the output files (and location) are named by Galaxy. It isn't enough to just have the output files in the right output directory. Looking at the documentation of phyml it seems you can't set your own output file names. This means you will have to write a wrapper that renames the files after the tool has run - or contact the author to include options to specify output file names. A wrapper can be as simple as a bashscript that executes the tool and after a succesful finish renames the output files to the output file names Galaxy provides (as described in the tool configuration xml - ts.3E_tag_set) Cheers, Jelle 2011/8/26 liyanhui607 <>:
ADD COMMENTlink written 7.3 years ago by Jelle Scholtalbers360
Hi Jelle, Thank you very much for your help ! Best! Yan-Hui Li
ADD REPLYlink written 7.3 years ago by liyanhui60720
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 158 users visited in the last hour