From b37f1e59811d08a747dded89cdc377a0c2607504 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Mon, 10 Jul 2023 10:02:12 +0200
Subject: [PATCH] Dockerfile for panacota users
---
PanACoTA/annotate_module/annotation_functions.py | 2 +-
containers/Dockerfile | 16 ++++++++--------
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/PanACoTA/annotate_module/annotation_functions.py b/PanACoTA/annotate_module/annotation_functions.py
index 81846f0f..df61768f 100755
--- a/PanACoTA/annotate_module/annotation_functions.py
+++ b/PanACoTA/annotate_module/annotation_functions.py
@@ -246,7 +246,7 @@ def prodigal_train(gpath, annot_folder):
logger=logger)
prodigalf.close()
prodigalferr.close()
- if ret.returncode == 0:
+ if ret != 1 and ret.returncode == 0:
logger.log(utils.detail_lvl(), f"End training on {gpath}")
return gpath_train
else:
diff --git a/containers/Dockerfile b/containers/Dockerfile
index d67e3997..542879d8 100644
--- a/containers/Dockerfile
+++ b/containers/Dockerfile
@@ -157,11 +157,11 @@ RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
# # # Install PanACoTA
-# # WORKDIR /install-dir
-# # RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/1.4.0.tar.gz
-# # RUN tar -xzf v1.4.0.tar.gz
-# # WORKDIR /install-dir/PanACoTA-1.4.0
-# # RUN ./make
-
-# # ENTRYPOINT ["/usr/local/bin/PanACoTA"]
-# # CMD ['-h']
\ No newline at end of file
+WORKDIR /install-dir
+RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/v1.4.0.tar.gz
+RUN tar -xzf v1.4.0.tar.gz
+WORKDIR /install-dir/PanACoTA-1.4.0
+RUN ./make
+
+ENTRYPOINT ["/usr/local/bin/PanACoTA"]
+CMD ['-h']
\ No newline at end of file
--
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