allow emmtyper to run via singularity

Daniel-VM · Jul 29, 2024 · 71f0aee · 71f0aee
1 parent 071ffe7
commit 71f0aee
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
@@ -36,7 +36,6 @@ gzip -dkc \$file > data_NC/\$(basename "\$file" .gz)
 
 EOF
 
-# FIXME: conda & singularity load
 # STEP 2: Setup exe file to perform unzip and emmtyper.
 cat <<EOF > _01_emmtyper.sbatch
 #!/bin/bash
@@ -50,28 +49,35 @@ cat <<EOF > _01_emmtyper.sbatch
 #SBATCH --output ./$(date '+%Y%m%d')_emmtyper.log
 
 # module load singularity
-# conda activate emmtyper-0.2.0
 
 # create results folder
 mkdir -p 01-typing
 mkdir -p 01-typing/tmps
+blastdb_path=/data/bi/references/cdc_emm_blastdb
 
 # Run emmtyper
-emmtyper \\
+singularity exec \\
+    --bind ${scratch_dir} \\
+    --bind ${scratch_dir}/../../ \\
+    --bind  \$blastdb_path \\
+    /data/bi/pipelines/singularity-images/singularity-emmtyper.0.2.0--py_0 emmtyper \\
     -w blast \\
     --keep \\
-    --blast_db '/data/bi/references/cdc_emm_blastdb/cdc_emm_database29042024' \\
+    --blast_db "${blastdb_path}/cdc_emm_database29042024" \\
     --percent-identity 95 \\
     --culling-limit 5 \\
     --output 01-typing/results_emmtyper.out \\
     --output-format verbose \\
     ./data_NC/*.fasta
 
-mv *emmtyper.log 01-typing/
 mv *.tmp 01-typing/tmps
 
 EOF
 
+# Bash script that performs all steps above
 echo "#!/bin/bash" > _ALLSTEPS_emmtyper.sh
+echo "# # module load singularity" >> _ALLSTEPS_emmtyper.sh
 echo "unzip_job_id=\$(sbatch _00_unzip_jobarray.sbatch | awk '{print \$4}')" >> _ALLSTEPS_emmtyper.sh
 echo "sbatch --dependency=afterok:\${unzip_job_id} _01_emmtyper.sbatch" >> _ALLSTEPS_emmtyper.sh
+
+chmod +x _ALLSTEPS_emmtyper.sh