From d8aa76953cf14036515bf8841c90210bf6d2470f Mon Sep 17 00:00:00 2001
From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:23:59 -0400
Subject: [PATCH] Update TRTools to v6.0.2 (#171)

* Update TRTools to v6

* try changing micromamba download link

* trying to fix version

* hard code 6.0.2

* unhard code

* try ver

* lint check

* EOF

* revert to version

* revert to VERSION
---
 images.toml               | 2 +-
 images/trtools/Dockerfile | 9 +++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/images.toml b/images.toml
index aebbc4a..8be0d6b 100644
--- a/images.toml
+++ b/images.toml
@@ -42,7 +42,7 @@ star = '2.7.10b'
 strvctvre = 'v.1.10'
 subread = '2.0.6'
 talos = '6.1.0'  # release to build, image names should have specific releases. Can build by naming side-branch
-trtools = '5.0.2'
+trtools = '6.0.2'
 trtools_hope_version = 'skip-if-monomorphic'  # specific branch name
 vep_105 = '105.0'
 vep_110 = 'release_110.1'
diff --git a/images/trtools/Dockerfile b/images/trtools/Dockerfile
index 3e05611..d4e4901 100644
--- a/images/trtools/Dockerfile
+++ b/images/trtools/Dockerfile
@@ -2,12 +2,13 @@ FROM debian:buster-slim
 
 ENV MAMBA_ROOT_PREFIX /root/micromamba
 ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
-ARG VERSION=${VERSION:-5.0.2}
+ARG VERSION=${VERSION:-6.0.2}
 
-RUN apt-get update && apt-get install -y git wget bash bzip2 zip && \
+# Install necessary packages
+RUN apt-get update && apt-get install -y git curl bash bzip2 zip && \
     rm -r /var/lib/apt/lists/* && \
-    rm -r /var/cache/apt/* && \
-    wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \
+    rm -r /var/cache/apt/*
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && \
     mkdir ${MAMBA_ROOT_PREFIX} && \
     micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \
     trtools=${VERSION} && \