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comparison sra_pileup.xml @ 2:f256cb398262 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author iuc
date Fri, 16 Sep 2016 17:24:03 -0400
parents b723c120161a
children 4732693f4661
comparison
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1:462ee06c9358 2:f256cb398262
1 <tool id="sra_pileup" name="Generate pileup format" version="1.2.5"> 1 <tool id="sra_pileup" name="Generate pileup format" version="2.6.2">
2 <description>from NCBI sra.</description> 2 <description>from NCBI sra.</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>sra-pileup --version</version_command> 7 <version_command>sra-pileup --version</version_command>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ## Need to set the home directory to the current working directory, 10 ## Need to set the home directory to the current working directory,
11 ## else the tool tries to write to home/.ncbi and fails when used 11 ## else the tool tries to write to home/.ncbi and fails when used
12 ## with a cluster manager. 12 ## with a cluster manager.
13 export HOME=\$PWD && 13 export HOME=\$PWD &&
14 vdb-config --restore-defaults && 14 vdb-config --restore-defaults &&
15 vdb-config -s "/repository/user/main/public/root=\$PWD" && 15 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
16 #if ( str( $adv.region ) == "" ): 16 #if ( str( $adv.region ) == "" ):
17 ASCP_PATH=`command -v ascp` && 17 ASCP_PATH=`command -v ascp` &&