Add docker build tests

.github/workflows/docker-release.yml

@@ -29,6 +29,9 @@ jobs:
           context: .
           load: true
           tags: digger:test
+      - name: Test
+        run: |
+          docker run --rm digger:test run_docker_tests
       - name: Build and push
         uses: docker/build-push-action@v4
         with:

run_docker_tests

@@ -0,0 +1,29 @@
+#!/bin/sh
+
+cd /digger/tests/human/IGH/verify
+
+bash -x run_digger.bat
+
+rv=$?  
+if [[ $rv != 0 ]]  
+then    
+    echo "Test failed."  
+    exit 1	
+fi
+
+if [ ! -f "IMGT000035.csv" ]; then
+    echo "Output not created."
+	exit 1
+fi
+
+diff model_IMGT000035.csv IMGT000035.csv
+
+rv=$?  
+if [[ $rv != 0 ]]  
+then    
+    echo "Output does not match expected content"  
+    exit 1	
+fi
+
+echo "Test passed."
+exit 0

tests/human/IGH/verify/README.txt

@@ -0,0 +1 @@
+This is a deliberately truncated version of IMGT000035 intended to be used to test Docker builds

tests/human/IGH/verify/comparison_results.txt

@@ -0,0 +1,27 @@
+
+
+type: V
+Functional sequences reported by digger but not by IMGT:
+4969,5264  imgt_match: IGHV7-81*01  imgt_func: ORF digger_match: IGHV7-81*01  digger_func: functional  notes: 
+469062,469353  imgt_match: IGHV3-38*02  imgt_func: ORF digger_match: IGHV3-38*02  digger_func: functional  notes: 
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:
+
+
+type: D
+Functional sequences reported by digger but not by IMGT:
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:
+
+
+type: J
+Functional sequences reported by digger but not by IMGT:
+1014594,1014646  imgt_match: IGHJ2*01  imgt_func: ORF digger_match: IGHJ2*01  digger_func: functional  notes: 
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:

tests/human/IGH/verify/comparison_results_notes.txt

@@ -0,0 +1,30 @@
+
+
+type: V
+Functional sequences reported by digger but not by IMGT:
+4969,5264  imgt_match: IGHV7-81*01  imgt_func: ORF digger_match: IGHV7-81*01  digger_func: functional  notes: 
+..imgt: noncanonical V-HEPTAMER: caccatg instead of cacagtg, noncanonical V-NONAMER: tcagaaatc instead of acacaaacc
+469062,469353  imgt_match: IGHV3-38*02  imgt_func: ORF digger_match: IGHV3-38*02  digger_func: functional  notes: 
+..imgt:  this gene has not been found rearranged (non-annotation difference).
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:
+
+
+type: D
+Functional sequences reported by digger but not by IMGT:
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:
+
+
+type: J
+Functional sequences reported by digger but not by IMGT:
+1014594,1014646  imgt_match: IGHJ2*01  imgt_func: ORF digger_match: IGHJ2*01  digger_func: functional  notes: 
+...currently listed in the IMGT reference set as functional (but annotated as ORF/non-canonical heptamer in this assembly)
+
+Functional sequences reported by IMGT but not by digger:
+
+Functional sequences reported by both IMGT and digger but with different sequences:

tests/human/IGH/verify/run_digger.bat

@@ -0,0 +1,15 @@
+mkdir work
+cd work
+extract_refs -L IGH "Homo sapiens"
+cat Homo_sapiens_IGHV.fasta Homo_sapiens_IGHD.fasta Homo_sapiens_IGHJ.fasta > Homo_sapiens_IGHVDJ.fasta
+
+parse_imgt_annotations --save_sequence IMGT000035.fasta "https://www.imgt.org/ligmdb/view?format=IMGT&id=BK063799" IMGT000035_genes.csv IGH
+
+head -n 1 IMGT000035.fasta >IMGT000035_trunc.fasta
+at_coords IMGT000035.fasta 1 15000 >>IMGT000035_trunc.fasta
+
+digger IMGT000035_trunc.fasta -keepwf -v_ref Homo_sapiens_IGHV.fasta -d_ref Homo_sapiens_IGHD.fasta -j_ref Homo_sapiens_IGHJ.fasta -v_ref_gapped Homo_sapiens_IGHV_gapped.fasta -ref imgt,Homo_sapiens_IGHVDJ.fasta -species human IMGT000035.csv
+
+cp IMGT000035_trunc.csv ..
+
+cd ..