Commit f1bda3f2 authored by Takadonet's avatar Takadonet

update to lastest code base in development branch

parent 60be1ca5
......@@ -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="1.3.6">
<package name="snvphyl" version="1.3.7">
<install version="1.0">
<actions>
<action type="setup_perl_environment">
......@@ -31,7 +31,7 @@
<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 5df23f0e4edec4c44cc9e7b3b78fd9fbf61d3378</action>
<action type="shell_command">git checkout 6fb98ccaf4a01cb23bbbe1e65a16e63dd7e1a907</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 ="0.0.3">
<description>Identify number of positions excluded based on filtered status</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<tool id="filtervcf" name="Filter vcf" version ="0.0.2">
<description>filter out indels and complex SNPS</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/filterVcf.pl --noindels $vcf
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
<tool id="findrepeat" name="Find Repeats" version ="0.0.3">
<description>Identify repeat elements using Mummer</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">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="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="mummer" version="3.23">
......
<tool id="snpmatrix" name="SNP Matrix" version ="0.0.2">
<description>Create SNP matrix from Phylip file</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<tool id="snvphyl_reporter" name="Snvphyl Reporter" version="1.1">
<description>Runs Snvphyl reporter</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">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="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="bcftools" version="1.2">
......
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.13">
<description>create a pseudo alignment from multiple VCFs files</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
</requirements>
<stdio>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.6">
<package name="snvphyl" version="1.3.7">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="samtools" version="0.1.19">
......
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.3">
<description>Checks the mapping quality of all BAM files generated in the core SNP pipeline.</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
<requirement type="package" version="1.3.7">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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