Merge pull request #452 from RECETOX/hechth-patch-7

Update matchms_formatter.xml with OPENBLAS_NUM_THREADS=1
RECETOX · Dec 1, 2023 · ad718c9 · ad718c9
2 parents ad60bf8 + cbfe659
commit ad718c9
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Showing 4 changed files with 21 additions and 6 deletions.
diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>reformat scores object of matchms to long format table</description>
 
     <macros>
@@ -24,6 +24,7 @@
     <environment_variables>
         <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
         <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+        <environment_variable name="OPENBLAS_NUM_THREADS">1</environment_variable>
     </environment_variables>
 
     <configfiles>

diff --git a/tools/matchms/matchms_metadata_merge.xml b/tools/matchms/matchms_metadata_merge.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_merge" name="matchms metadata merge" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_metadata_merge" name="matchms metadata merge" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Merge metadata csv into MSP by a specified column</description>
 
     <macros>
@@ -16,11 +16,15 @@
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
-
+    
     <command detect_errors='aggressive'><![CDATA[
         python3 '${matchms_python_cli}'
     ]]></command>
 
+    <environment_variables>
+        <environment_variable name="OPENBLAS_NUM_THREADS">1</environment_variable>
+    </environment_variables>
+
 <configfiles>
 <configfile name="matchms_python_cli">
 import pandas

diff --git a/tools/matchms/matchms_subsetting.xml b/tools/matchms/matchms_subsetting.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_subsetting" name="matchms subsetting" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_subsetting" name="matchms subsetting" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Extract spectra from a library given unique metadata identifier</description>
 
     <macros>
@@ -21,6 +21,10 @@
         python3 '${matchms_python_cli}'
     ]]></command>
 
+    <environment_variables>
+        <environment_variable name="OPENBLAS_NUM_THREADS">1</environment_variable>
+    </environment_variables>
+
 <configfiles>
 <configfile name="matchms_python_cli">
 import pandas
@@ -104,4 +108,4 @@ matchms.exporting.save_as_msp(filtered_spectra.tolist(), '${output}')
     <citations>
         <citation type="doi">https://doi.org/10.5281/zenodo.8083373</citation>
     </citations>
-</tool>
+</tool>
diff --git a/tools/rem_complex/rem_complex.xml b/tools/rem_complex/rem_complex.xml
@@ -1,4 +1,4 @@
-<tool id="rem_complex" name="Remove coordination complexes" version="@TOOL_VERSION@+galaxy0"  profile="21.09">
+<tool id="rem_complex" name="Remove coordination complexes" version="@TOOL_VERSION@+galaxy1"  profile="21.09">
     <description>Remove molecular coordination complexes from a list of structure representations</description>
     <macros>
         <import>macros.xml</import>
@@ -7,12 +7,18 @@
         <requirement type="package" version="1.5.3">pandas</requirement>
         <requirement type="package" version="3.1.1">openbabel</requirement>
     </requirements>
+
     <command detect_errors="exit_code"><![CDATA[
         python  $__tool_directory__/rem_complex.py
         -i '${input}'
         -iformat '${input.ext}'
         -o '${output}' 
     ]]></command>
+
+    <environment_variables>
+        <environment_variable name="OPENBLAS_NUM_THREADS">1</environment_variable>
+    </environment_variables>
+
     <inputs>
         <param name="input" format="inchi,smi,csv" type="data" help="Accepted input formats: CSV, SMI, and InChI."/>
     </inputs>