Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 22:2680041530ec draft

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author jeremie
date Fri, 20 Jun 2014 06:28:21 -0400
parents 7b71d14e0f78
children 302ce0e59304
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21:7b71d14e0f78 22:2680041530ec
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.18"> 3 <package name="samtools" version="0.1.18">
4 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True" />
5 </package> 5 </package>
6 <package name="pindel" version="0.2.5"> 6 <package name="pindel" version="0.2.5">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> --> 9 <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> -->
23 <action type="shell_command"> 23 <action type="shell_command">
24 echo "SAMTOOLS= 24 echo "SAMTOOLS=
25 THREADS= 25 THREADS=
26 COLOUSINGBD15_TIME=60 26 COLOUSINGBD15_TIME=60
27 COLOWOBD15_TIME=80 27 COLOWOBD15_TIME=80
28 SIM1CHRVS20305_TIME=60" >> Makefile.local 28 SIM1CHRVS20305_TIME=60" > Makefile.local
29 </action> 29 </action>
30 <action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action> 30 <action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
31 <!-- <action type="shell_command">./INSTALL ~/samtools</action> --> 31 <!-- <action type="shell_command">./INSTALL ~/samtools</action> -->
32 32
33 33