Mercurial > repos > bgruening > trna_prediction

comparison tool_dependencies.xml @ 1:d788d1abe238 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 22 Jan 2015 13:15:51 -0500
parents d34f31cbc9dd
children
comparison
equal deleted inserted replaced
0:d34f31cbc9dd 1:d788d1abe238
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="biopython" version="1.61"> 3 <package name="biopython" version="1.61">
4 <repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="aragorn" version="1.2.36"> 6 <package name="aragorn" version="1.2.36">
7 <install version="1.0"> 7 <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 <actions>
9 <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action>
10 <action type="make_directory">$INSTALL_DIR/bin/</action>
11 <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action>
12 <action type="move_file">
13 <source>aragorn</source>
14 <destination>$INSTALL_DIR/bin</destination>
15 </action>
16 <action type="set_environment">
17 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
18 </action>
19 </actions>
20 </install>
21 <readme>Compiling ARAGORN requires gcc.</readme>
22 </package> 8 </package>
23 <package name="tRNAscan-SE" version="1.3.1"> 9 <package name="tRNAscan-SE" version="1.3.1">
24 <install version="1.0"> 10 <repository changeset_revision="a3fb2752c340" name="package_trnascan_1_3_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
25 <actions>
26 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
27 <action type="make_directory">$INSTALL_DIR/bin/</action>
28 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
29 <action type="make_directory">$INSTALL_DIR/man/</action>
30 <!-- replacing the hardcoded pathvariables with the real ones -->
31 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; sed 's%^BINDIR = .*%BINDIR = $INSTALL_DIR/bin/%' Makefile | sed 's%^LIBDIR = .*%LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/%' | sed 's%^MANDIR = .*%MANDIR = $INSTALL_DIR/man%' &gt; Makefile_new</action>
32 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
33 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make &amp;&amp; make install</action>
34
35 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
36 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
37 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
38 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
39 <action type="set_environment">
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
41 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/bin/</environment_variable>
42 </action>
43 </actions>
44 </install>
45 <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
46 </package> 11 </package>
12 <set_environment version="1.0">
13 <environment_variable action="set_to" name="TRNAPRED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
14 </set_environment>
47 </tool_dependency> 15 </tool_dependency>