Mercurial > repos > morinlab > ensembl_vep

changeset 0:ba310f592561 draft

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Uploaded
author morinlab
date Sat, 03 Dec 2016 18:56:30 -0500
parents
children 9d4894e61812
files tool_dependencies.xml
diffstat 1 files changed, 44 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Dec 03 18:56:30 2016 -0500
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+<?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" />
+    </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" />
+    </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>
+    </package>
+</tool_dependency>