Changed to miniforge environment

.shed.yml

@@ -0,0 +1,12 @@
+name: autoBIGS
+owner: RealYHD
+description: Automated MLST typing from PubMLST and InstitutPasteur.
+homepage_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
+long_description: |
+  A program that allows quickly batched requests for obtaining MLST 
+  profiles on multiple FASTA sequences and exporting it as a convenient 
+  CSV. Capable of querying a variety of MLST databases from both 
+  Institut Pasteur and PubMLST.
+remote_repository_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
+categories:
+- Sequence Analysis

Jenkinsfile

@@ -2,19 +2,19 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'pip'
+            defaultContainer 'miniforge3'
-            inheritFrom 'pip'
+            inheritFrom 'miniforge'
         }
     }
     
     stages {
         stage ("install") {
             steps {
+                sh 'conda install python==3.12.7 pip -y -q'
                 sh 'useradd galaxy -m'
                 sh 'apt-get update'
                 sh 'apt-get install sudo -y'
-                sh 'sudo -u galaxy pip install -r requirements.txt'
+                sh 'pip install -r requirements.txt'
-                sh 'sudo -u galaxy pip install standard-imghdr'
             }
         }
         stage ("lint") {

autobigs-cli.xml

@@ -19,7 +19,7 @@
 					autoBIGS info --retrieve-bigsdbs --csv $info_db_out
 				#end if
 			#else if $mode.operation == "st":
-				autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
+				autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
 			#end if
 	]]></command>
 	<inputs>
@@ -45,7 +45,9 @@
 				</conditional>
 			</when>
 			<when value="st">
-				<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
+				<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"/>
@@ -66,7 +68,9 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="operation" value="st" />
-            <param name="fastas" value="tohama_I_bpertussis_wgs.fasta" />
+			<repeat name="fastas_list">
+	            <param name="fasta" value="tohama_I_bpertussis_wgs.fasta" />
+			</repeat>
             <param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
             <param name="schema" value="3" />
             <output name="mlst_profiles_output" file="tohama_I_bpertussis_wgs_typed.csv" ftype="csv" />
@@ -96,17 +100,19 @@
     </tests>
 	<help><![CDATA[
 
-usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]]
+usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]] [--csv CSV_OUTPUT]
 
 Fetches the latest BIGSdb MLST database definitions.
 
 options:
   -h, --help            show this help message and exit
-  --retrieve-bigsdbs    Lists all known BIGSdb MLST databases (fetched from known APIs and cached).
+  --retrieve-bigsdbs, -l
-  --retrieve-bigsdb-schemas SCHEMA_IDS
+                        Lists all known BIGSdb MLST databases (fetched from known APIs and cached).
+  --retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS
                         Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given.
+  --csv, -o CSV_OUTPUT  Output list as CSV at a given path. A suffix is added depending on the action taken.
 
-usage: autoBIGS st [-h] [--exact] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
+usage: autoBIGS st [-h] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
 
 Returns MLST exact profile matches.
 
@@ -118,10 +124,7 @@ 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
+  --stop-on-fail, -sof  Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches).
-                        expecting exact matches).
-
-
 	]]></help>
     <citations>
         <citation type="bibtex">