From 64c88e53e19a898633a1a8e6fed381c4d2ff3bf6 Mon Sep 17 00:00:00 2001
From: taylorpaisie <tpaisie91@gmail.com>
Date: Mon, 25 Nov 2024 12:57:11 -0500
Subject: [PATCH] updating CAT dockerfile tests

---
 CAT/5.3/Dockerfile | 24 +++++++++++++++++++++---
 CAT/5.3/README.md  | 12 ++++++------
 2 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/CAT/5.3/Dockerfile b/CAT/5.3/Dockerfile
index 22e284b9a..8e48c5b39 100644
--- a/CAT/5.3/Dockerfile
+++ b/CAT/5.3/Dockerfile
@@ -8,7 +8,7 @@ ARG CAT_VER
 ARG DIAMOND_VER
 
 LABEL base.image="ubuntu:focal"
-LABEL dockerfile.version="2"
+LABEL dockerfile.version="1"
 LABEL software="CAT"
 LABEL software.version=${CAT_VER}
 LABEL description="CAT: a tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)."
@@ -65,6 +65,14 @@ FROM app AS test
 
 WORKDIR /data/test
 
+RUN wget -nv --no-check-certificate \
+    https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/checkm2/1.0.2/burk_wgs.fa \
+    -O burk_wgs_pos_ctrl.fa &&\
+    wget -nv --no-check-certificate \
+    https://merenlab.org/data/refining-mags/files/GN02_MAG_IV_B_1-contigs.fa \
+    -O GN02_MAG_IV_B_1-contigs.fa
+
+
 # Prepare testing database
 RUN mkdir -p db_tests && \
     gzip -d /CAT/tests/data/prepare/small.fa.gz && \
@@ -74,8 +82,18 @@ RUN mkdir -p db_tests && \
     --nodes /CAT/tests/data/prepare/nodes.dmp \
     --db_dir db_tests/
 
+# Running CAT on contigs
+RUN CAT contigs -c burk_wgs_pos_ctrl.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+
+# Running BAT on a set of MAGs
+RUN CAT bins -b GN02_MAG_IV_B_1-contigs.fa \
+    -d db_tests/db \
+    -t db_tests/tax
+
 # Run CAT test
-RUN CAT contigs -c /CAT/tests/data/contigs/small_contigs.fa \
-    -d db_tests/db/ -t db_tests/tax/
+# RUN CAT contigs -c /CAT/tests/data/contigs/small_contigs.fa \
+#     -d db_tests/db/ -t db_tests/tax/
 
 WORKDIR /data
diff --git a/CAT/5.3/README.md b/CAT/5.3/README.md
index 2adb06225..02d1cc96e 100644
--- a/CAT/5.3/README.md
+++ b/CAT/5.3/README.md
@@ -26,12 +26,12 @@ wget -nv --no-check-certificate https://merenlab.org/data/refining-mags/files/GN
 Use CAT and BAT for taxonomic classification for both best datasets:
 ```
 # Running CAT on contigs
-CAT contigs -c burk_wgs_pos_ctrl.fa \
-    -d /$LAB_HOME/.databases/CAT/20231120_CAT_nr/db \
-    -t /$LAB_HOME/.databases/CAT/20231120_CAT_nr/tax
+CAT contigs -c test/burk_wgs_pos_ctrl.fa \
+    -d db_tests/db \
+    -t db_tests/tax
 
 # Running BAT on a set of MAGs
-CAT bins -b GN02_MAG_IV_B_1-contigs.fa \
-    -d /$LAB_HOME/.databases/CAT/20231120_CAT_nr/db \
-    -t /$LAB_HOME/.databases/CAT/20231120_CAT_nr/tax
+CAT bins -b test/GN02_MAG_IV_B_1-contigs.fa \
+    -d db_tests/db \
+    -t db_tests/tax
 ```