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Add phylonco and lphybeast to 2.6 packages #122

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merged 2 commits into from
Apr 13, 2023
Merged

Add phylonco and lphybeast to 2.6 packages #122

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b78158d
Update phylonco packages extra description
kche309 Apr 13, 2023
0b3e3a9
Add phylonco and lphybeast to 2.6
kche309 Apr 13, 2023
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12 changes: 6 additions & 6 deletions packages-extra.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -322,25 +322,25 @@
<depends on='FastRelaxedClockLogNormal' atleast='1.1.0'/>
</package>

<package name='Phylonco' version='0.0.4'
<package name='phylonco' version='0.0.4'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.4.zip"
description="Phylonco - a package for single cell cancer analysis"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.5'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>

<package name='Phylonco' version='0.0.5'
<package name='phylonco' version='0.0.5'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.5.zip"
description="Phylonco - a package for single cell cancer analysis"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.5'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>

<package name='Phylonco' version='0.0.6'
<package name='phylonco' version='0.0.6'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.6.zip"
description="Phylonco - a package for single cell cancer analysis"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.6'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
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149 changes: 149 additions & 0 deletions packages2.6.xml
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Expand Up @@ -529,7 +529,156 @@
projectURL="https://github.com/mrc-ide/PhyDyn">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>


<package name='phylonco' version='0.0.4'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.4.zip"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.5'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>

<package name='phylonco' version='0.0.5'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.5.zip"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.5'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>

<package name='phylonco' version='0.0.6'
url="https://github.com/bioDS/beast-phylonco/raw/master/dist/phylonco.addon.v0.0.6.zip"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.6'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='lphybeast' atleast='0.3.0'/>
</package>

<package name='phylonco' version='0.0.7'
url="https://github.com/bioDS/beast-phylonco/releases/download/v0.0.7-pre/phylonco-addon-0.0.7.zip"
description="A package for single cell cancer evolution"
projectURL="https://github.com/bioDS/beast-phylonco">
<depends on='beast2' atleast='2.6.7'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='lphybeast' atleast='0.4.1'/>
</package>

<package name="lphybeast" version="0.3.1"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/lphybeast/0.3.1/lphybeast-0.3.1.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeast"
description="A command-line program that takes an LPhy model specification including a data block,
and produces a BEAST 2 XML input file.">
<depends on='beast2' atleast='2.6.6'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='feast' atleast='7.9.1'
projectURL="https://github.com/tgvaughan/feast"
description="Expands the flexibility of BEAST 2 XML."/>

<depends on='BEAST_CLASSIC' atleast='1.5.0'/>
<depends on='SSM' atleast='1.1.0'
description="Standard Nucleotide Substitution Models"
projectURL="https://github.com/BEAST2-Dev/substmodels/"/>
<depends on='MM' atleast='1.1.1'
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological character evolution"/>
<depends on='SA' atleast='2.0.2'
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees"/>
<depends on='Mascot' atleast='2.1.2'
description="Marginal approximation of the structured coalescent"
projectURL="https://taming-the-beast.org/tutorials/Mascot-Tutorial/"/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
</package>

<package name="lphybeast" version="0.4.0"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/lphybeast/0.4.0/lphybeast-0.4.0.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeast"
description="A command-line program that takes an LPhy model specification including a data block,
and produces a BEAST 2 XML input file.">
<depends on='beast2' atleast='2.6.7'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='feast' atleast='7.11.0'
projectURL="https://github.com/tgvaughan/feast"
description="Expands the flexibility of BEAST 2 XML."/>
<depends on='BEAST_CLASSIC' atleast='1.5.0'/>
<depends on='SSM' atleast='1.1.0'
description="Standard Nucleotide Substitution Models"
projectURL="https://github.com/BEAST2-Dev/substmodels/"/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
</package>

<package name="lphybeast" version="0.4.1"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/lphybeast/0.4.1/lphybeast-0.4.1.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeast"
description="A command-line program that takes an LPhy model specification including a data block,
and produces a BEAST 2 XML input file.">
<depends on='beast2' atleast='2.6.7'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='feast' atleast='7.11.0'
projectURL="https://github.com/tgvaughan/feast"
description="Expands the flexibility of BEAST 2 XML."/>
<depends on='BEAST_CLASSIC' atleast='1.5.0'/>
<depends on='SSM' atleast='1.1.0'
description="Standard Nucleotide Substitution Models"
projectURL="https://github.com/BEAST2-Dev/substmodels/"/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
</package>

<!-- url="https://s01.oss.sonatype.org/content/repositories/releases/io/github/linguaphylo/lphybeast/0.4.1/lphybeast-0.4.1.zip" -->
<package name="lphybeast" version="0.4.2"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/lphybeast/0.4.2/lphybeast-0.4.2.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeast"
description="A command-line program that takes an LPhy model specification including a data block,
and produces a BEAST 2 XML input file.">
<depends on='beast2' atleast='2.6.7'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='feast' atleast='7.11.0'
projectURL="https://github.com/tgvaughan/feast"
description="Expands the flexibility of BEAST 2 XML."/>
<depends on='BEAST_CLASSIC' atleast='1.5.0'/>
<depends on='SSM' atleast='1.1.0'
description="Standard Nucleotide Substitution Models"
projectURL="https://github.com/BEAST2-Dev/substmodels/"/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
</package>

<package name="LPhyBeastExt" version="0.1.0"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/LPhyBeastExt/0.1.0/LPhyBeastExt-0.1.0.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeastExt"
description="An extension of LPhyBEAST.">
<depends on='lphybeast' atleast='0.4.1'/>

<depends on='Mascot' atleast='2.1.2'
description="Marginal approximation of the structured coalescent"
projectURL="https://taming-the-beast.org/tutorials/Mascot-Tutorial/"/>
<depends on='MM' atleast='1.1.1'
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological character evolution"/>
<depends on='SA' atleast='2.0.2'
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees"/>
</package>

<package name="LPhyBeastExt" version="0.1.1"
url="https://repo.maven.apache.org/maven2/io/github/linguaphylo/LPhyBeastExt/0.1.1/LPhyBeastExt-0.1.1.zip"
projectURL="https://github.com/LinguaPhylo/LPhyBeastExt"
description="An extension of LPhyBEAST.">
<depends on='lphybeast' atleast='0.4.2'/>

<depends on='Mascot' atleast='2.1.2'
description="Marginal approximation of the structured coalescent"
projectURL="https://taming-the-beast.org/tutorials/Mascot-Tutorial/"/>
<depends on='MM' atleast='1.1.1'
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological character evolution"/>
<depends on='SA' atleast='2.0.2'
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees"/>
</package>


<package name='SSM' version='1.1.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/SSM/SSM.v1.1.0.zip"
description="Standard Nucleotide Substitution Models"
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