Singularity: make HIVIntact the default and the only app

Singularity

@@ -3,7 +3,7 @@ Bootstrap: docker
 From: ubuntu:22.04
 
 %help
-    Search proviral consensus sequences for primers, then use HIVSeqinR to
+    Search proviral consensus sequences for primers, then use HIVIntact to
     decide if the genomes are complete.
 
     This Singularity container can be run on Kive: http://cfe-lab.github.io/Kive
@@ -46,31 +46,11 @@ From: ubuntu:22.04
     echo ===== Installing minimap2 ===== >/dev/null
     apt-get install -y minimap2
 
-    echo ===== Installing hivseqinr ===== >/dev/null
-    apt-get install -y libz-dev libcurl4-openssl-dev libxml2-dev
-    DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base
-    Rscript /opt/primer_finder/gene_splicer/configure_r.sh
-    python3 -m gene_splicer.hivseqinr /opt/hivseqinr
-
     # Clean up
     apt-get remove -y wget git build-essential
 
 %environment
     export LANG=en_US.UTF-8
 
 %runscript
-    gene_splicer_sample --hivseqinr /opt/hivseqinr "$@"
-
-%apprun hivintact
     gene_splicer_sample --hivintact "$@"
-
-%apphelp hivintact
-    Search proviral consensus sequences for primers, then use HIVIntact to
-    decide if the genomes are complete.
-
-%applabels hivintact
-    KIVE_INPUTS sample_info_csv contigs_csv conseqs_csv cascade_csv
-    KIVE_OUTPUTS outcome_summary_csv conseqs_primers_csv contigs_primers_csv \
-        table_precursor_csv hivseqinr_results_tar
-    KIVE_THREADS 1
-    KIVE_MEMORY 200