why the result files are empty ? and is java applet supported by galaxy system?
Hi All, We want to add a program “PhyML 3.0” to galaxy system. This software was for phylogenetic developed byhttp://www.atgc-montpellier.fr/phyml/binaries.php.It can run normally in Linux environment with a file for example named “sample” as input and two files automatically named “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” 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/000”, 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
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 - http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_...) Cheers, Jelle 2011/8/26 liyanhui607 <liyanhui607@163.com>:
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Hi All,
We want to add a program “PhyML 3.0” to galaxy system. This software was for phylogenetic developed by http://www.atgc-montpellier.fr/phyml/binaries.php. It can run normally in Linux environment with a file for example named “sample” as input and two files automatically named “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” 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/000”, 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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hi Jelle, Thank you very much for your help ! Best! Yan-Hui Li At 2011-08-26 16:09:16,"Jelle Scholtalbers" <j.scholtalbers@gmail.com> 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 - http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_...)
Cheers, Jelle
2011/8/26 liyanhui607 <liyanhui607@163.com>:
===> Please use "Reply All" when responding to this email! <===
Hi All,
We want to add a program “PhyML 3.0” to galaxy system. This software was for phylogenetic developed by http://www.atgc-montpellier.fr/phyml/binaries.php. It can run normally in Linux environment with a file for example named “sample” as input and two files automatically named “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” 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/000”, 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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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liyanhui607