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comparison tool_dependencies.xml @ 2:00d73c812399 draft

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Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.
author pjbriggs
date Wed, 22 Mar 2017 11:36:07 -0400
parents 02a01ea54722
children
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1:02a01ea54722 2:00d73c812399
6 </package> 6 </package>
7 <package name="R" version="3.1.2"> 7 <package name="R" version="3.1.2">
8 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 8 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package> 9 </package>
10 <!-- Subset of UCSC tools --> 10 <!-- Subset of UCSC tools -->
11 <package name="ucsc_tools_for_macs21" version="1.0"> 11 <package name="ucsc_tools_for_macs21" version="2.0">
12 <install version="1.0"> 12 <install version="1.0">
13 <actions> 13 <actions>
14 <!-- fetchChromSizes --> 14 <!-- fetchChromSizes -->
15 <action type="download_binary"> 15 <action type="download_binary">
16 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template> 16 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
22 <action type="download_binary"> 22 <action type="download_binary">
23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template> 23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
24 </action> 24 </action>
25 <action type="chmod"> 25 <action type="chmod">
26 <file mode="755">$INSTALL_DIR/bedClip</file> 26 <file mode="755">$INSTALL_DIR/bedClip</file>
27 </action>
28 <!-- bedSort -->
29 <action type="download_binary">
30 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort</url_template>
31 </action>
32 <action type="chmod">
33 <file mode="755">$INSTALL_DIR/bedSort</file>
27 </action> 34 </action>
28 <!-- bedGraphToBigWig --> 35 <!-- bedGraphToBigWig -->
29 <action type="download_binary"> 36 <action type="download_binary">
30 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> 37 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
31 </action> 38 </action>