Commit 278d82fe authored by Takadonet's avatar Takadonet

updated to latest version of the code base on development branch. Added inital...

updated to latest version of the code base on development branch. Added inital suite_snvphyl to enable easier download
parent 59c5b8ba
......@@ -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="1.2">
<package name="snvphyl" version="1.3">
<install version="1.0">
<actions>
<action type="setup_perl_environment">
......@@ -20,12 +20,13 @@
<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>
<package>https://cpan.metacpan.org/authors/id/C/CH/CHORNY/Switch-2.17.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 f2396b267002ccc5696d9fecb583e000dc26fe75</action>
<action type="shell_command">git checkout e26ea1d15785be9bfaaad9cd2fdbefc57b27646f</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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.2">
<package name="snvphyl" version="1.3">
<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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/filterVcf.pl --noindels $vcf
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.2">
<package name="snvphyl" version="1.3">
<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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">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="1.2">
<package name="snvphyl" version="1.3">
<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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
</requirements>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.2">
<package name="snvphyl" version="1.3">
<repository name="package_snvphyl" owner="phil" />
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.2">
<package name="snvphyl" version="1.3">
<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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
</requirements>
<stdio>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.2">
<package name="snvphyl" version="1.3">
<repository name="package_snvphyl" owner="phil" />
</package>
<package name="samtools" version="0.1.19">
<repository name="package_samtools_0_1_19" owner="ericenns" />
<repository name="package_samtools_0_1_19" owner="iuc" />
</package>
</tool_dependency>
<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="1.2">snvphyl</requirement>
<requirement type="package" version="1.3">snvphyl</requirement>
<requirement type="package" version="5.18.1">perl</requirement>
<requirement type="package" version="0.1.19">samtools</requirement>
</requirements>
......
<?xml version="1.1"?>
<repositories description="A suite of tools associated with SNVphyl pipeline">
<repository name="smalt_map" owner="jen-cabral" />
<repository name="smalt_index" owner="jen-cabral"/>
<repository name="freebayes" owner="phil"/>
<repository name="samtools_mpileup" owner="devteam"/>
<repository name="bcftools_view" owner="takadonet"/>
<repository name="bcftools_call" owner="phil"/>
<repository name="filter_vcf" owner="phil"/>
<repository name="snp_matrix" owner="phil"/>
<repository name="find_repeats" owner="phil"/>
<repository name="vcf2pseudoalignment" owner="phil"/>
<repository name="phyml" owner="phil"/>
<repository name="bcf_bgzip_datatype" owner="takadonet"/>
<repository name="msa_datatypes" owner="iuc"/>
<repository name="verify_map" owner="phil"/>
<repository name="filter_stats" owner="phil"/>
</repositories>
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