Mercurial > repos > biomonika > linkyx
changeset 17:2cbcdfd5d489
added perl dependencies
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Wed, 10 Sep 2014 12:48:34 -0400 |
| parents | 373cd706d44f |
| children | 8673c6f733d1 |
| files | LINKYX_identify_X_linked_SNPs.xml LINKYX_identify_Y_linked_SNPs.xml LINKYX_mpileup_wrapper.xml LINKYX_reformat_trinity_header.xml tool_dependencies.xml |
| diffstat | 5 files changed, 31 insertions(+), 10 deletions(-) [+] |
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--- a/LINKYX_identify_X_linked_SNPs.xml Wed Sep 10 11:40:09 2014 -0400 +++ b/LINKYX_identify_X_linked_SNPs.xml Wed Sep 10 12:48:34 2014 -0400 @@ -3,8 +3,9 @@ <requirements> <requirement type="set_environment">LINKYX_PATH</requirement> <requirement type="set_environment">SAMTOOLS</requirement> - <requirement type="set_environment">PERL_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="1.6.922">bioperl</requirement> </requirements> <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5</command> <inputs>
--- a/LINKYX_identify_Y_linked_SNPs.xml Wed Sep 10 11:40:09 2014 -0400 +++ b/LINKYX_identify_Y_linked_SNPs.xml Wed Sep 10 12:48:34 2014 -0400 @@ -3,8 +3,9 @@ <requirements> <requirement type="set_environment">LINKYX_PATH</requirement> <requirement type="set_environment">SAMTOOLS</requirement> - <requirement type="set_environment">PERL_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="1.6.922">bioperl</requirement> </requirements> <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command> <inputs>
--- a/LINKYX_mpileup_wrapper.xml Wed Sep 10 11:40:09 2014 -0400 +++ b/LINKYX_mpileup_wrapper.xml Wed Sep 10 12:48:34 2014 -0400 @@ -3,8 +3,9 @@ <requirements> <requirement type="set_environment">LINKYX_PATH</requirement> <requirement type="set_environment">SAMTOOLS</requirement> - <requirement type="set_environment">PERL_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="1.6.922">bioperl</requirement> </requirements> <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command> <inputs>
--- a/LINKYX_reformat_trinity_header.xml Wed Sep 10 11:40:09 2014 -0400 +++ b/LINKYX_reformat_trinity_header.xml Wed Sep 10 12:48:34 2014 -0400 @@ -3,8 +3,9 @@ <requirements> <requirement type="set_environment">LINKYX_PATH</requirement> <requirement type="set_environment">SAMTOOLS</requirement> - <requirement type="set_environment">PERL_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="1.6.922">bioperl</requirement> </requirements> <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command> <inputs>
--- a/tool_dependencies.xml Wed Sep 10 11:40:09 2014 -0400 +++ b/tool_dependencies.xml Wed Sep 10 12:48:34 2014 -0400 @@ -2,6 +2,22 @@ <set_environment version="1.0"> <environment_variable name="LINKYX_PATH" action="set_to">$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> + <package name="perl" version="5.18.1"> <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" /> </package> @@ -9,16 +25,16 @@ <install version="1.0"> <actions> <action type="setup_perl_environment"> - <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 changeset_revision="091a97f8c585" 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>Bio::DB::Sam</package> - <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package> + <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::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>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package> + <package>Bio::DB::Sam</package> + <package>PerlIO::gzip</package> </action> </actions> </install> @@ -26,4 +42,5 @@ Bundle::BioPerl </readme> </package> + </tool_dependency> \ No newline at end of file