Commit 172eca22 authored by Takadonet's avatar Takadonet

switched to newest code base that includes bug fixes for vcf2core and changes...

switched to newest code base that includes bug fixes for vcf2core and changes to vcf2pseudoalignment
parent 01566894
......@@ -3,7 +3,7 @@
<package name="perl" version="5.18.1">
<repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
</package>
<package name="snvphyl" version="1.3.5">
<package name="snvphyl" version="1.3.6">
<install version="1.0">
<actions>
<action type="setup_perl_environment">
......@@ -26,13 +26,12 @@
<package>https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Test-Simple-1.001014.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/O/OV/OVID/Text-Diff-1.41.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/T/TY/TYEMQ/Algorithm-Diff-1.1903.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/S/SA/SANKO/Readonly-2.00.tar.gz</package>
</action>
<action type="change_directory">../</action>
<action type="shell_command">git clone http://irida.corefacility.ca/gitlab/analysis-pipelines/snvphyl-tools.git</action>
<action type="change_directory">snvphyl-tools</action>
<action type="shell_command">git checkout f49a1e9f098c83e1e50d705b153b15579ddf91a7</action>
<action type="shell_command">git checkout 5df23f0e4edec4c44cc9e7b3b78fd9fbf61d3378</action>
<action type="change_directory">bcfplugins/bcftools-1.2</action>
<action type="shell_command">make</action>
<action type="change_directory">../..</action>
......
<tool id="filterstat" name="Filter Stats" version ="0.0.2">
<tool id="filterstat" name="Filter Stats" version ="0.0.3">
<description>Identify number of positions excluded based on filtered status</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<tool id="filtervcf" name="Filter vcf" version ="0.0.1">
<tool id="filtervcf" name="Filter vcf" version ="0.0.2">
<description>filter out indels and complex SNPS</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/filterVcf.pl --noindels $vcf
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
<tool id="findrepeat" name="Find Repeats" version ="0.0.2-dev">
<tool id="findrepeat" name="Find Repeats" version ="0.0.3">
<description>Identify repeat elements using Mummer</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="3.23">mummer</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="mummer" version="3.23">
......
<tool id="snpmatrix" name="SNP Matrix" version ="0.0.1">
<tool id="snpmatrix" name="SNP Matrix" version ="0.0.2">
<description>Create SNP matrix from Phylip file</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<tool id="snvphyl_reporter" name="Snvphyl Reporter" version="1.0">
<tool id="snvphyl_reporter" name="Snvphyl Reporter" version="1.1">
<description>Runs Snvphyl reporter</description>
<requirements>
<requirement type="package" version="1.3.5">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/reporter.pl --step bam_quality_data --output $output
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.5">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="bcftools" version="1.2">
......
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.11">
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.12">
<description>create a pseudo alignment from multiple VCFs files</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
</requirements>
<stdio>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.1">
<package name="snvphyl" version="1.3.6">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="samtools" version="0.1.19">
......
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.2">
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.3">
<description>Checks the mapping quality of all BAM files generated in the core SNP pipeline.</description>
<requirements>
<requirement type="package" version="1.3.1">snvphyl</requirement>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
<requirement type="package" version="0.1.19">samtools</requirement>
</requirements>
......
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