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author sarahinraauzeville
date Tue, 12 Dec 2017 09:40:48 -0500
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************************************************************************************
******        Add perl and xml wrapper files in tools/ d                      ******
************************************************************************************


Download files with hg clone in tools/ directory, then you have these files availables (wrappers and scripts):
sm_dos2unix.pl  sm_dos2unix.xml
and GalaxyPath.pm

Add GalaxyPath.pm file in /path/to/galaxy_sources/ directory

************************************************************************************
******        tool_conf.xml file to update                                    ******
************************************************************************************

Add a tag <tool> in your section "convert formats" (for instance) in your config/tool_conf.xml file:
        <tool file="my_tools/sm_dos2unix/sm_dos2unix.xml" />

************************************************************************************
******        Add paths in galaxy.ini configuation file                       ******
************************************************************************************

Add a my_bin/ directory in galaxy repository with symbolic links to binaries:
[galaxy-preprod@vm-galaxy-preprod my_bin]$ pwd
/galaxydata/galaxy-preprod/my_bin
lrwxrwxrwx  1 galaxy-prod wbioinfo   11  3 juin   2016 dos2unix -> dos2unix3.1


Add paths to binaries and a section [workPath], at the end of galaxy.ini file: 
Dans geany ../../config/galaxy.ini &
DOS=/galaxydata/galaxy-prod/my_bin/dos2unix