Mercurial > repos > yhoogstrate > featurecounts

comparison tool_dependencies.xml @ 6:fae19d64e9de draft

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Uploaded
author yhoogstrate
date Thu, 13 Nov 2014 09:46:22 -0500
parents 9fcffbe6c206
children 2312bedfe2a3
comparison
equal deleted inserted replaced
5:31279ea9fbfa 6:fae19d64e9de
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.4-source.tar.gz &amp;&amp; cd subread-1.4.4-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action> 6 <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.4-source.tar.gz &amp;&amp; cd subread-1.4.4-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action>
7 <action type="move_file"> 7 <action type="move_file">
8 <source>../subread-1.4.4-source/bin/featureCounts</source> 8 <source>../subread-1.4.4-source/bin/featureCounts</source>
9 <destination>$INSTALL_DIR/bin</destination> 9 <destination>$INSTALL_DIR/bin/</destination>
10 </action> 10 </action>
11 <action type="set_environment"> 11 <action type="set_environment">
12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
13 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> 13 <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
14 </action> 14 </action>
15 </actions> 15 </actions>
16 </install> 16 </install>
17 <readme> 17 <readme>
18 Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed! 18 Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
19 </readme> 19 </readme>
20 </package> 20 </package>
21 21
22 <package name="featurecounts2bed" version="1.0.0"> 22 <package name="featurecounts2bed" version="1.0.0">
23 <install version="1.0"> 23 <install version="1.0">
24 <actions> 24 <actions>
25 <action type="move_file">
26 <source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source>
27 <destination>$INSTALL_DIR/bin/</destination>
28 </action>
29 <!--
30 Revert to the previous if the move command doesn't work
31
25 <action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh &amp;&amp; chmod 755 *.sh</action> 32 <action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh &amp;&amp; chmod 755 *.sh</action>
26 <action type="move_file"> 33 <action type="move_file">
27 <source>../featurecounts2bed.sh</source> 34 <source>../featurecounts2bed.sh</source>
28 <destination>$INSTALL_DIR/bin</destination> 35 <destination>$INSTALL_DIR/bin</destination>
29 </action> 36 </action>
37 -->
38 <action type="chmod">
39 <file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
40 </action>
30 <action type="set_environment"> 41 <action type="set_environment">
31 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 42 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
32 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
33 </action> 43 </action>
34 </actions> 44 </actions>
35 </install> 45 </install>
36 </package> 46 </package>
37 </tool_dependency> 47 </tool_dependency>