rename all config dirs to avoid conflicts when running parallel tasks… (

#6041) * rename all config dirs to avoid conflicts when running parallel tasks in galaxy workflow * upgrade tool version suffix * Update macros.xml * Update dimet_timecourse_analysis.xml * Update dimet_pca_plot.xml * Update dimet_pca_analysis.xml * Update dimet_pca_analysis.xml * Update dimet_metabologram.xml * Update dimet_metabologram.xml * Update dimet_isotopologues_plot.xml * Update dimet_isotopologues_plot.xml * Update dimet_enrichment_plot.xml * Update dimet_differential_multigroup_analysis.xml * Update dimet_differential_multigroup_analysis.xml * Update dimet_differential_analysis.xml * Update dimet_bivariate_analysis.xml * Update dimet_abundance_plot.xml * replace __new_file_path__ by temp directory in job working directory * replace back temp by __new_file_path__ directory in job working directory * replace back temp by __new_file_path__ directory in job working directory * put back the ./config dir in macros.xml, remoce -cp option in hydra args and replace ++hydra.run.dir=XXXXX by ++hydra.run.dir=. --------- Co-authored-by: M Bernt <[email protected]>
galaxyproject · Jun 21, 2024 · 3dba874 · 3dba874
1 parent d28dc08
commit 3dba874
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Showing 11 changed files with 23 additions and 35 deletions.
diff --git a/tools/dimet/dimet_abundance_plot.xml b/tools/dimet/dimet_abundance_plot.xml
@@ -15,8 +15,7 @@
     @INIT_TIMEPOINTS@
     @INIT_ENRICHMENT_METABOLITES@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=abundance_plot'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -232,4 +231,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_bivariate_analysis.xml b/tools/dimet/dimet_bivariate_analysis.xml
@@ -13,8 +13,7 @@
     @INIT_BI_ANALYSIS@
     @INIT_BIVAR_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=bivariate_analysis'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -272,4 +271,4 @@ You can also use the minimal data examples from https://zenodo.org/records/10579
  ]]>
     </help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_differential_analysis.xml b/tools/dimet/dimet_differential_analysis.xml
@@ -15,8 +15,7 @@
     @INIT_GROUPS@
     @INIT_DIFF_ANALYSIS_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=differential_analysis'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -305,4 +304,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_differential_multigroup_analysis.xml b/tools/dimet/dimet_differential_multigroup_analysis.xml
@@ -17,8 +17,7 @@
     @INIT_TIMEPOINTS@
     @INIT_MULTIGROUP_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=multi_group_comparison'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -262,4 +261,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_enrichment_plot.xml b/tools/dimet/dimet_enrichment_plot.xml
@@ -15,8 +15,7 @@
     @INIT_TIMEPOINTS@
     @INIT_ENRICHMENT_METABOLITES@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=mean_enrichment_line_plot'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -242,4 +241,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_isotopologues_plot.xml b/tools/dimet/dimet_isotopologues_plot.xml
@@ -14,8 +14,7 @@
     @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=isotopologue_proportions_plot'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -254,4 +253,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_metabologram.xml b/tools/dimet/dimet_metabologram.xml
@@ -16,10 +16,9 @@
     @INIT_PATHWAYS@
     @INIT_STAT_TEST@
     HYDRA_FULL_ERROR=1 python -m dimet
-    -cp '$__new_file_path__/config'
+    '++hydra.run.dir=.'
     '++figure_path=figures'
     '++table_path=tables'
-    '++hydra.run.dir=metabologram'
     '++analysis={
         dataset:{
             _target_: dimet.data.DataIntegrationConfig,
@@ -344,4 +343,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations" />
-</tool> 
+</tool> 
diff --git a/tools/dimet/dimet_pca_analysis.xml b/tools/dimet/dimet_pca_analysis.xml
@@ -14,8 +14,7 @@
     @INIT_IMPUTE_VALUES@
     @INIT_CONDITIONS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=pca-analysis-tables'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -212,4 +211,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_pca_plot.xml b/tools/dimet/dimet_pca_plot.xml
@@ -14,8 +14,7 @@
     @INIT_IMPUTE_VALUES@
     @INIT_CONDITIONS@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
-        '++hydra.run.dir=pca-plot'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
         '++analysis={
@@ -50,7 +49,6 @@
             '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
         #end if
     @REMOVE_CONFIG@
-
     ]]></command>
     <inputs>
         <expand macro="input_parameters_pca"/>
@@ -240,4 +238,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798
  ]]>
     </help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/dimet/dimet_timecourse_analysis.xml b/tools/dimet/dimet_timecourse_analysis.xml
@@ -15,10 +15,9 @@
     @INIT_GROUPS@
     @INIT_CONDITIONS_TIMECOURSE@
     HYDRA_FULL_ERROR=1 python -m dimet
-        -cp '$__new_file_path__/config'
+        '++hydra.run.dir=.'
         '++figure_path=figures'
         '++table_path=tables'
-        '++hydra.run.dir=time_course_analysis'
         '++analysis={
             dataset:{
                 _target_: dimet.data.DatasetConfig,

diff --git a/tools/dimet/macros.xml b/tools/dimet/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.4</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
@@ -598,16 +598,15 @@
 
     ]]></token>
     <token name="@INIT_CONFIG@"><![CDATA[
-    mkdir -p '$__new_file_path__/config' &&
-    touch '$__new_file_path__/config/config.yaml' &&
+    mkdir -p 'config' &&
+    touch 'config/config.yaml' &&
     ]]></token>
     <token name="@REMOVE_CONFIG@"><![CDATA[
-    && rm -r '$__new_file_path__/config'
+    && rm -r 'config'
     ]]></token>
     <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
 
     mkdir -p data &&
-
     #if $metadata_path:
         ln -s '$metadata_path' data/metadata.csv &&
     #end if