Mercurial > repos > biomonika > linkyx
changeset 16:373cd706d44f
toolshed15
author | biomonika <biomonika@psu.edu> |
---|---|
date | Wed, 10 Sep 2014 11:40:09 -0400 |
parents | a4f2492ce714 |
children | 2cbcdfd5d489 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 7 insertions(+), 18 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Sep 10 11:30:31 2014 -0400 +++ b/tool_dependencies.xml Wed Sep 10 11:40:09 2014 -0400 @@ -2,34 +2,23 @@ <set_environment version="1.0"> <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - - <package name="samtools" version="0.1.19"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> - <action type="shell_command">sed -i 's/O2/O2 -fPIC/' Makefile</action> - <action type="shell_command">make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme> + <package name="perl" version="5.18.1"> + <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" /> </package> <package name="bioperl" version="1.6.922"> <install version="1.0"> <actions> <action type="setup_perl_environment"> - <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="perl" version="5.18.1" /> </repository> <!-- allow downloading and installing an Perl package from cpan.org--> - <package>XML::Parser</package> - <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package> + <package>Bio::DB::Sam</package> + <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package> <package>Bio::DB::Fasta</package> + <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package> <package>File::Slurp</package> - <package>Bio::DB::Sam</package> + <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package> </action> </actions> </install>