Mercurial > repos > biomonika > test_dependency

annotate tool_dependencies.xml @ 8:5573c2fa9824

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
full depend
author biomonika <biomonika@psu.edu>
date Mon, 25 Aug 2014 12:51:30 -0400
parents 7112ee9a7ada
children 480491c2ce1c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 <tool_dependency>
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 <set_environment version="1.0">
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 </set_environment>
8
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
5 <package name="samtools_fPIC" version="1.1">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
6 <install version="1.0">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
7 <actions>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
8 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
9 <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile </action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
10 <action type="shell_command">make </action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
11 <action type="make_directory">$INSTALL_DIR/bin</action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
12 <action type="set_environment">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
13 <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
14 </action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
15 </actions>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
16 </install>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
17 <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
18 </package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
19
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
20 <package name="perl" version="5.18.1">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
21 <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
22 </package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
23
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
24 <package name="bioperl" version="1.6.922">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
25 <install version="1.0">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
26 <actions>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
27 <action type="setup_perl_environment">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
28 <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
29 <package name="perl" version="5.18.1" />
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
30 </repository>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
31 <!-- allow downloading and installing an Perl package from cpan.org-->
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
32 <package>Bio::DB::Sam</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
33 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
34 <package>Bio::DB::Fasta</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
35 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
36 <package>File::Slurp</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
37 <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
38 </action>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
39 </actions>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
40 </install>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
41 <readme>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
42 Installing dependencies. Bio::DB::Sam needs to know location of bam.h and compiled libbam.a files, therefore environmental variable SAMTOOLS needs to be correctly set.
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
43 </readme>
5573c2fa9824 full depend
biomonika <biomonika@psu.edu>
parents: 0
diff changeset
44 </package>
0
biomonika <biomonika@psu.edu>
parents:
diff changeset
45 </tool_dependency>