Mercurial > repos > geert-vandeweyer > vcf_to_variantdb
changeset 5:6ddc1c6472ef draft
Macro corrections
| author | geert-vandeweyer |
|---|---|
| date | Fri, 21 Feb 2014 06:38:35 -0500 |
| parents | 7ebc71784e9f |
| children | 775372e00f55 |
| files | VCF_to_VariantDB.pl VCF_to_VariantDB_macros.xml readme.rst tool_dependencies.xml |
| diffstat | 4 files changed, 3 insertions(+), 27 deletions(-) [+] |
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--- a/VCF_to_VariantDB.pl Wed Feb 19 06:53:47 2014 -0500 +++ b/VCF_to_VariantDB.pl Fri Feb 21 06:38:35 2014 -0500 @@ -81,6 +81,8 @@ die("ERROR: $content"); } +print $opts{'H'}. " was specified as galaxy host\n"; + ############################################### ## SEND THE VCF AND BAM FILES FOR PROCESSING ## ###############################################
--- a/VCF_to_VariantDB_macros.xml Wed Feb 19 06:53:47 2014 -0500 +++ b/VCF_to_VariantDB_macros.xml Fri Feb 21 06:38:35 2014 -0500 @@ -6,6 +6,6 @@ </requirements> </xml> <token name="@URL@"> - "\$GALAXY_URL/" + $GALAXY_URL/ </token> </macros>
--- a/readme.rst Wed Feb 19 06:53:47 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -Galaxy wrapper for VariantDB Import -=================================== - -This wrapper and VariantDB is written by Geert Vandeweyer. - -The recommended installation is by means of the toolshed_. - -.. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/vcf_to_variantdb - -Galaxy should be able to install the needed perl module dependencies automatically -for you. To allow your server to communicate with VariantDB, you must edit the GALAXY_URL environment variable in the file: - -<tool_dependency_dir>/environment_settings/GALAXY_URL/geert-vandeweyer/vcf_to_variantdb/<hash_string>/env.sh - -to point to the full URL of the server (e.g: http://biominavm-galaxy.biomina.be/galaxy ) where you have installed the wrapper. - -Finally, if you also have a private VariantDB instance, you need to add it to the wrapper configuration file, as an extra option.
--- a/tool_dependencies.xml Wed Feb 19 06:53:47 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="GALAXY_URL">http://your.galaxy.server/and_sub_path/</environment_variable> - </set_environment> - <package name="perl_module_libwww" version="6.05"> - <repository changeset_revision="f217bf3faf3b" name="package_perl_libwww" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>