Mercurial > repos > morinlab > ensembl_vep

changeset 3:7d471de72765 draft

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Uploaded
author morinlab
date Fri, 27 Jan 2017 16:40:30 -0500
parents 0124502b307f
children 276b9ad6081f
files tool_dependencies.xml
diffstat 1 files changed, 6 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jan 27 16:40:18 2017 -0500
+++ b/tool_dependencies.xml	Fri Jan 27 16:40:30 2017 -0500
@@ -1,44 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="perl" version="5.18.1">
-        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a8d909fa1465" name="package_perl_5_18" owner="morinlab" toolshed="http://galaxy-morinlab.mbb.sfu.ca:9009" />
+    </package>
+    <package name="mysql" version="6.1.0">
+        <repository changeset_revision="1acb2ddf2097" name="package_mysql_6_1_0" owner="morinlab" toolshed="http://galaxy-morinlab.mbb.sfu.ca:9009" />
     </package>
     <package name="ensembl_vep_perl_env" version="84">
-        <repository changeset_revision="9976000ce924" name="package_ensembl_vep_perl_environment_84" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1a757c9a8d34" name="package_ensembl_vep_perl_environment_84" owner="morinlab" toolshed="http://galaxy-morinlab.mbb.sfu.ca:9009" />
     </package>
     <package name="ensembl_vep" version="84">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://github.com/Ensembl/ensembl-tools/tarball/release/84.tar.gz</action>
-                <action type="set_environment_for_install">
-                     <repository changeset_revision="9976000ce924" name="package_ensembl_vep_perl_environment_84" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                          <package name="ensembl_vep_perl_env" version="84" />
-                     </repository>
-                </action>
-		<action type="shell_command">mkdir $INSTALL_DIR/cache</action>
-                <action type="shell_command">mkdir $INSTALL_DIR/cache/tmp</action>
-                <action type="shell_command">chmod 777 $INSTALL_DIR/cache</action>
-                <action type="shell_command">chmod 777 $INSTALL_DIR/cache/tmp</action>
-                <action type="move_directory_files">
-                    <source_directory>scripts/variant_effect_predictor</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="ENSEMBL_VEP_84_INSTALL_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/Bio</environment_variable>
-                </action>
-                <action type="shell_command">echo 'y' | perl $INSTALL_DIR/INSTALL.pl --DESTDIR $INSTALL_DIR -q --AUTO a</action>
-            </actions>
-        </install>
-        <readme>
-This package installs the Ensembl Variant Effect Predictor (VEP) and its dependencies.
-
-At the moment, this package assumes that the appropriate Perl 5 environment is properly set up prior to installation. Notably, this includes the following modules:
-- LWP::Simple
-- Archive::Zip
-- DBD::mysql
-
-Also, the cache is downloaded seperately and its location is stored in the ENSEMBL_VEP_84_CACHE_DIR environment variable.
-        </readme>
+        <repository changeset_revision="a890339bb9b6" name="package_ensembl_vep_84" owner="morinlab" toolshed="http://galaxy-morinlab.mbb.sfu.ca:9009" />
     </package>
 </tool_dependency>