Commit 59c5b8ba authored by Takadonet's avatar Takadonet

updated all wrapper to use latest package_snvphyl with bug fixes

parent 32d41332
......@@ -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="1.1">
<package name="snvphyl" version="1.2">
<install version="1.0">
<actions>
<action type="setup_perl_environment">
......@@ -16,12 +16,16 @@
<package>https://cpan.metacpan.org/authors/id/A/AJ/AJPAGE/Bio-Pipeline-Comparison-1.123050.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.410.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-0.042.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/JSON-2.90.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/O/OV/OVID/Test-JSON-0.11.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/M/MI/MIKO/String-Util-1.24.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.200.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 71a865f8b8dc4ddcf3a604565fe436ae011decba</action>
<action type="shell_command">git checkout f2396b267002ccc5696d9fecb583e000dc26fe75</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 ="0.0.1">
<description>Identify number of positions excluded based on filtered status</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<tool id="filtervcf" name="Filter vcf" version ="0.0.1">
<description>filter out indels and complex SNPS</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/filterVcf.pl --noindels $vcf
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
<tool id="findrepeat" name="Find Repeats" version ="0.0.2-dev">
<description>Identify repeat elements using Mummer</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">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="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="mummer" version="3.23">
......
<tool id="snpmatrix" name="SNP Matrix" version ="0.0.1">
<description>Create SNP matrix from Phylip file</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="bcftools" version="1.2">
......
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.11">
<description>create a pseudo alignment from multiple VCFs files</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
</requirements>
<stdio>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.1">
<package name="snvphyl" version="1.2">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="samtools" version="0.1.19">
......
<tool id="verify_map" name="Verify Mapping Quality" version="0.0.1">
<description>Checks the mapping quality of all BAM files generated in the core SNP pipeline.</description>
<requirements>
<requirement type="package" version="1.1">snvphyl</requirement>
<requirement type="package" version="1.2">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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