Updating tools/bcftools from version 1.15.1 to 1.20

galaxyproject · Aug 22, 2024 · c9c609e · c9c609e
1 parent 06a9256
commit c9c609e
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/tools/bcftools/bcftools_call.xml b/tools/bcftools/bcftools_call.xml
@@ -1,4 +1,4 @@
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>

diff --git a/tools/bcftools/bcftools_consensus.xml b/tools/bcftools/bcftools_consensus.xml
@@ -8,7 +8,7 @@
     <expand macro="bio_tools" />
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
-        <requirement type="package" version="5.0.1">gawk</requirement>
+        <requirement type="package" version="5.3.0">gawk</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[

diff --git a/tools/bcftools/bcftools_mpileup.xml b/tools/bcftools/bcftools_mpileup.xml
@@ -1,4 +1,4 @@
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>

diff --git a/tools/bcftools/bcftools_norm.xml b/tools/bcftools/bcftools_norm.xml
@@ -9,7 +9,7 @@
         <expand macro="samtools_requirement"/>
         <!-- gawk only required for current bcftools norm bug workaround
         Remove once fixed (see command section below -->
-        <requirement type="package" version="5.0.1">gawk</requirement>
+        <requirement type="package" version="5.3.0">gawk</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[

diff --git a/tools/bcftools/bcftools_stats.xml b/tools/bcftools/bcftools_stats.xml
@@ -8,7 +8,7 @@
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
         <expand macro="matplotlib_requirement" />
-        <requirement type="package" version="0.12.0">tectonic</requirement>
+        <requirement type="package" version="0.15.0">tectonic</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[

diff --git a/tools/bcftools/macros.xml b/tools/bcftools/macros.xml
@@ -1,6 +1,6 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.15.1</token>
-  <token name="@VERSION_SUFFIX@">4</token>
+  <token name="@TOOL_VERSION@">1.20</token>
+  <token name="@VERSION_SUFFIX@">0</token>
   <token name="@PROFILE@">20.01</token>
   <xml name="bio_tools">
       <xrefs>
@@ -10,15 +10,15 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
-      <requirement type="package" version="1.15.1">htslib</requirement>
+      <requirement type="package" version="1.20">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.15.1">samtools</requirement>
+      <requirement type="package" version="1.20">samtools</requirement>
   </xml>
   <xml name="matplotlib_requirement">
-      <requirement type="package" version="3.5.3">matplotlib</requirement>
+      <requirement type="package" version="3.9.2">matplotlib</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>