Merge pull request #715 from RECETOX/singularity-imgs

hechth · web-flow · commit ad0d51ab9500 · 2025-12-12T10:41:15.000Z
for images prefer cerit-hosted singularity
diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
@@ -2,6 +2,7 @@
     <token name="@TOOL_VERSION@">5.2.1</token>
     <xml name="requirements">
         <requirements>
+            <container type="singularity">oras://cerit.io/galaxy/qcxms-docker:@TOOL_VERSION@</container>
             <container type="docker">recetox/qcxms-docker:@TOOL_VERSION@</container>
         </requirements>
     </xml>
diff --git a/tools/qcxms/qcxms_getres.xml b/tools/qcxms/qcxms_getres.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy3" profile="22.09">
+<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy4" profile="22.09">
     <description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>
diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy6" profile="22.09">
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy7" profile="22.09">
     <description>required as first step to prepare for the production runs</description>
     
     <macros>
diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy4" profile="22.09">
+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy5" profile="22.09">
     <description>Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>
diff --git a/tools/recetox_msfinder/macros.xml b/tools/recetox_msfinder/macros.xml
@@ -2,6 +2,7 @@
     <token name="@TOOL_VERSION@">v3.5.2</token>
     <xml name="requirements">
         <requirements>
+            <container type="singularity">oras://cerit.io/galaxy/recetox-msfinder:v3.5.2-rcx2</container>
             <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx2</container>
         </requirements>
     </xml>
diff --git a/tools/recetox_msfinder/recetox_msfinder.xml b/tools/recetox_msfinder/recetox_msfinder.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy4">
+<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy5">
     <description>Annotation of fragment peaks in mass spectral libraries.</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/retip/macros.xml b/tools/retip/macros.xml
@@ -28,6 +28,7 @@
 
     <xml name="requirements">
         <requirements>
+            <container type="singularity">oras://cerit.io/galaxy/retip:@TOOL_VERSION@-recetox4</container>
             <container type="docker">recetox/retip:@TOOL_VERSION@-recetox4</container>
         </requirements>
     </xml>
diff --git a/tools/retip/retip_apply.xml b/tools/retip/retip_apply.xml
@@ -1,4 +1,4 @@
-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy5">
+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy6">
     <description>is retention time predictor for Metabolomics</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/retip/retip_descriptors.xml b/tools/retip/retip_descriptors.xml
@@ -1,4 +1,4 @@
-<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy5">
+<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy6">
     <description>for retention time prediction</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/retip/retip_filter_rt.xml b/tools/retip/retip_filter_rt.xml
@@ -1,4 +1,4 @@
-<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy5">
+<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy6">
     <description>for predicted RT's</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/retip/retip_train.xml b/tools/retip/retip_train.xml
@@ -1,4 +1,4 @@
-<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy5">
+<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy6">
     <description>the Keras model to predict retention times</description>
     <macros>
         <import>macros.xml</import>

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy3" profile="22.09">`
	`1`	`+<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy4" profile="22.09">`
`2`	`2`	`<description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>`
`3`	`3`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy6" profile="22.09">`
	`1`	`+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy7" profile="22.09">`
`2`	`2`	`<description>required as first step to prepare for the production runs</description>`
`3`	`3`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy4" profile="22.09">`
	`1`	`+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy5" profile="22.09">`
`2`	`2`	`<description>Production run to obtain a QCxMS simulated mass spectrum</description>`
`3`	`3`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy4">`
	`1`	`+<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy5">`
`2`	`2`	`<description>Annotation of fragment peaks in mass spectral libraries.</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy5">`
	`1`	`+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy6">`
`2`	`2`	`<description>is retention time predictor for Metabolomics</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy5">`
	`1`	`+<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy6">`
`2`	`2`	`<description>for retention time prediction</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy5">`
	`1`	`+<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy6">`
`2`	`2`	`<description>for predicted RT's</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`