Revert "Use main.py in Singularity"

This reverts commit 6261b88.

Singularity

@@ -49,7 +49,6 @@ From: python:3.8
     micall/monitor    /opt/micall/micall/monitor
     micall/utils      /opt/micall/micall/utils
 
-    micall/main.py  /opt/micall/micall/
     README.md       /opt/micall/
     LICENSE.txt     /opt/micall/
     pyproject.toml  /opt/micall/
@@ -124,14 +123,14 @@ From: python:3.8
     pip install --upgrade pip
     pip install /opt/micall
     python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
-    micall make_blast_db
+    python /opt/micall/micall/blast_db/make_blast_db.py
 
 %environment
     export PATH=/opt/bowtie2:/bin:/usr/local/bin
     export LANG=en_US.UTF-8
 
 %runscript
-    micall micall_kive "$@"
+    python /opt/micall/micall/utils/micall_kive.py "$@"
 
 %apphelp filter_quality
     Post-processing of short-read alignments.
@@ -143,7 +142,7 @@ From: python:3.8
     KIVE_MEMORY 200
 
 %apprun filter_quality
-    micall filter_quality "$@"
+    PYTHONPATH=/opt/micall python -m micall.core.filter_quality "$@"
 
 %apphelp resistance
     Combine HCV results with HCV-Midi results, and generate resistance
@@ -157,7 +156,7 @@ From: python:3.8
     KIVE_MEMORY 200
 
 %apprun resistance
-    micall micall_kive_resistance "$@"
+    python /opt/micall/micall/utils/micall_kive_resistance.py "$@"
 
 %apprun denovo
     python /opt/micall/micall_kive.py --denovo "$@"