Mercurial > repos > rmarenco > hubarchivecreator

diff tool_dependencies.xml @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
parents
children df9e12da0d13
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jul 13 13:36:37 2016 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <!-- UCSC Tools in  -->
+    <!-- Useful for HAC are:
+        - twoBitInfo
+        - sort
+        - bedToBigBed
+        - gff3ToGenePred
+        - gtfToGenePred
+        - genePredToBed
+        - faToTwoBit
+        - samtools
+    -->
+    <package name="ucsc_tools" version="312">
+        <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <!-- TODO: Tools to install -->
+    <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
+
+
+    <!-- Package gff3ToGenePred -->
+    <package name="gff3ToGenePred" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    <!-- Package gtfToGenePred -->
+    <package name="gtfToGenePred" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    <!-- Package genePredToBed -->
+    <package name="genePredToBed" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+</tool_dependency>