diff --git a/Jenkinsfile b/Jenkinsfile
index 9f3b18a..95dc19d 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -2,29 +2,27 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'miniforge3'
-            inheritFrom 'miniforge'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
         }
     }
     
     stages {
         stage ("install") {
             steps {
-                sh 'conda env update -n base --file environment.yml'
-                sh 'useradd galaxy -m'
-                sh 'apt-get update'
-                sh 'apt-get install sudo -y'
+                sh 'pip install -r requirements.txt'
+                sh 'planemo ci_setup'
             }
         }
         stage ("lint") {
             steps {
-                sh "sudo -u galaxy planemo lint autobigs-cli.xml"
+                sh "planemo lint autobigs-cli.xml"
             }
         }
         stage ("test") {
             steps {
-                sh 'sudo -u galaxy mkdir test_results'
-                sh "sudo -u galaxy planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
+                sh 'mkdir test_results'
+                sh "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
                 xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
             }
         }
diff --git a/autobigs-cli.xml b/autobigs-cli.xml
index 20afb44..3d82a2d 100644
--- a/autobigs-cli.xml
+++ b/autobigs-cli.xml
@@ -1,76 +1,76 @@
 <tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-	<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
-	<macros>
-		<token name="@TOOL_VERSION@">0.5.0</token>
-		<token name="@VERSION_SUFFIX@">0</token>
-    	<import>autobigs-cli_macros.xml</import>
-	    <expand macro="bio_tools"/>
-	</macros>
+    <description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.5.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <import>autobigs-cli_macros.xml</import>
+        <expand macro="bio_tools"/>
+    </macros>
 
-	<requirements>
-		<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
-	</requirements>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
+    </requirements>
 
-	<command detect_errors="exit_code"><![CDATA[
-			#if $mode.operation == "info":
-				#if $mode.select_info.retrieved == "schemes":
-					autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
-				#else if $mode.select_info.retrieved == "databases":
-					autoBIGS info --retrieve-bigsdbs --csv $info_db_out
-				#end if
-			#else if $mode.operation == "st":
-				autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
-			#end if
-	]]></command>
-	<inputs>
-		<conditional name="mode">
-			<param name="operation" label="Operation" type="select">
-				<option value="info">Retrieve Database Information</option>
-				<option value="st">Perform Sequence Typing</option>
-			</param>
-			<when value="info">
-				<conditional name="select_info">
-					<param name="retrieved" label="Schemes or Database List" type="select">
-						<option value="schemes">Available Schemas for Database</option>
-						<option value="databases">Available Databases</option>
-					</param>
-					<when value="schemes">
-						<repeat name="schemes_list" title="Schemes" min="1">
-							<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
-						</repeat>
-					</when>
-					<when value="databases">
+    <command detect_errors="exit_code"><![CDATA[
+            #if $mode.operation == "info":
+                #if $mode.select_info.retrieved == "schemes":
+                    autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
+                #else if $mode.select_info.retrieved == "databases":
+                    autoBIGS info --retrieve-bigsdbs --csv $info_db_out
+                #end if
+            #else if $mode.operation == "st":
+                autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
+            #end if
+    ]]></command>
+    <inputs>
+        <conditional name="mode">
+            <param name="operation" label="Operation" type="select">
+                <option value="info">Retrieve Database Information</option>
+                <option value="st">Perform Sequence Typing</option>
+            </param>
+            <when value="info">
+                <conditional name="select_info">
+                    <param name="retrieved" label="Schemes or Database List" type="select">
+                        <option value="schemes">Available Schemas for Database</option>
+                        <option value="databases">Available Databases</option>
+                    </param>
+                    <when value="schemes">
+                        <repeat name="schemes_list" title="Schemes" min="1">
+                            <param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
+                        </repeat>
+                    </when>
+                    <when value="databases">
 
-					</when>
-				</conditional>
-			</when>
-			<when value="st">
-				<repeat name="fastas_list" title="Fasta" min="1">
-					<param name="fasta" label="FASTA file" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
-				</repeat>
-				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
-				<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
-				<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
-			</when>
-		</conditional>
-	</inputs>
-	<outputs>
-		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
-			<filter>mode['operation'] == 'st'</filter>
-		</data>
-		<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
-			<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
-		</data>
-		<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
-			<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
-		</data>
-	</outputs>
+                    </when>
+                </conditional>
+            </when>
+            <when value="st">
+                <repeat name="fastas_list" title="Fasta" min="1">
+                    <param name="fasta" label="FASTA file" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
+                </repeat>
+                <param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
+                <param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
+                <param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
+            <filter>mode['operation'] == 'st'</filter>
+        </data>
+        <data name="info_db_out" label="${tool.name} supported Databases" format="csv">
+            <filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
+        </data>
+        <data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
+            <filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
+        </data>
+    </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="operation" value="st" />
-			<repeat name="fastas_list">
-	            <param name="fasta" value="tohama_I_minimized_features.fasta" />
-			</repeat>
+            <repeat name="fastas_list">
+                <param name="fasta" value="tohama_I_minimized_features.fasta" />
+            </repeat>
             <param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
             <param name="schema" value="3" />
             <output name="mlst_profiles_output" file="tohama_I_minimized_features_typed.csv" ftype="csv" />
@@ -79,26 +79,26 @@
             <param name="operation" value="info" />
             <param name="retrieved" value="databases" />
             <output name="info_db_out">
-				<assert_contents>
-					<has_text text="BIGSdb Names,Source"/>
-					<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
-				</assert_contents>
-			</output>
+                <assert_contents>
+                    <has_text text="BIGSdb Names,Source"/>
+                    <has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="operation" value="info" />
-			<repeat name="schemes_list">
-            	<param name="selected_db" value="pubmlst_bordetella_seqdef" />
-			</repeat>
+            <repeat name="schemes_list">
+                <param name="selected_db" value="pubmlst_bordetella_seqdef" />
+            </repeat>
             <output name="info_schemes_out">
-				<assert_contents>
-					<has_text text="Name,ID"/>
-					<has_text text="MLST,3"/>
-				</assert_contents>
-			</output>
+                <assert_contents>
+                    <has_text text="Name,ID"/>
+                    <has_text text="MLST,3"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
-	<help><![CDATA[
+    <help><![CDATA[
 
 usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]] [--csv CSV_OUTPUT]
 
@@ -125,7 +125,7 @@ positional arguments:
 options:
   -h, --help            show this help message and exit
   --stop-on-fail, -sof  Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches).
-	]]></help>
+    ]]></help>
     <citations>
         <citation type="bibtex">
 @book{Deng2025RealYHD,