[galaxy-dev] Problem with file's extension
Hi All, I have some problem with extension of file.some executables file will recognize the only the specific extension like autodock . it takes one input file ( extension with .dpf ) and one outpt file (extension with .dlg). how can we resolve such type of problem . Regards Shashi shekhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem with file's extension
Hi Shashi, You can add your own datatypes using the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes Thanks, K On Wed, May 25, 2011 at 1:05 PM, shashi shekhar meshash...@gmail.comwrote: Hi All, I have some problem with extension of file.some executables file will recognize the only the specific extension like autodock . it takes one input file ( extension with .dpf ) and one outpt file (extension with .dlg). how can we resolve such type of problem . Regards Shashi shekhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem with file's extension
Shashi, All of Galaxy's datasets have the extension .dat so your problem is not uncommon. The general solution to this is to create temp files that have the the required extensions for the tool and point them to/ from the actual Galaxy input and output. There are several ways to do this. If you have a wrapper script, you can do it there. See the BWA wrapper for an example in a Python wrapper (tools/sr_mapping/ bwa_wrapper.py, especially lines 223-8). If you have only the XML config file, you can do it there. For an example of this, see the Freebayes tool (tools/human_genome_variation/freebayes.xml). This links two input files to specifically named files. Let us know if you have further questions. Kelly On Wed May 25, at 1:05 PM, shashi shekhar wrote: Hi All, I have some problem with extension of file.some executables file will recognize the only the specific extension like autodock . it takes one input file ( extension with .dpf ) and one outpt file (extension with .dlg). how can we resolve such type of problem . Regards Shashi shekhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/